I’ve printed out this post so I can read it more carefully; goodness!

Two thoughts I wanted to offer right away, though, that I hope will be helpful:
1. The letter you referred to near the beginning that outlines the norms for what may/may not be used for the Eucharist, please note, was intended not for the world-wide Church but for bishops. Such a letter is for them, to inform them of what the Church asks of them; the pastoral application of these guidelines–which you seem to be most concerned with–is up to each bishop, since he ultimately is responsible for the care of the people in his diocese. While the letter may sound cold and mechanical to many, well, it’s supposed to; it is up to each bishop to determine how it will be applied to the local Church.
2. “To which I answer… really?” The quote you use above this, not to accuse you of anything, you’ve pulled off the website of a group that is actually in schism with the Church; in other words, they do not believe that Vatican II was a valid council and they do not believe that Pope John Paul II or Benedict XVI are valid popes. I just wanted to point that out since you are blogging not about groups who have broken communion with the Catholic Church, but rather all those Churches in communion with Rome (Roman Catholics, Byzantines, Maronites, Malchites, Syro-Malabars, some Anglicans, etc.).
Hopefully in a few days I’ll have more to offer! One thing your post does very well, though, is to illustrate how difficult it really is to debate whether or not something that is on the surface a small matter–wheat bread for the Eucharist–can be changed without being unfaithful or otherwise being in error. I think it is, truly, a complicated question, especially since Catholics believe that Jesus Himself instituted the Eucharist and He did so very intentionally, everything having its reason and place. To consider changing one thing SHOULD raise many questions! Beyond the theological concerns, however, your post hits the nail right on the head: the pastoral concerns are also important to consider. Some who have gluten allergies–like my mother–are such that they can suffer some gluten and in spite of the suffering it inflicts, their love for their Eucharistic Lord overcomes their aversion to all gluten. But there are some, too, for whom any amount of gluten is detrimental or even fatal (I suppose, in extreme cases). 
Anyways, more to come, I hope!

All right, brother, I have finally had a chance to read your post and to collect my thoughts a bit more. To keep things organized I thought I would present my thoughts point-by-point following your post according to its paragraphs, and then after all that maybe I’ll go on for a bit with my own thoughts. We’ll see what happens! Since you spend the first four paragraphs outlining your concern I’ll leave them; after all I’m not here trying to argue that you are wrong. My purpose here primarily is to try and help you to understand the “why” behind the Catholic reason for doing the things you are frustrated with, namely, why wheaten bread for the Eucharist is so important, specifically because refusing to give on the matter presents difficult and not unimportant pastoral concerns. So I will start with the quote you offered from the Council of Trent (please again note that you borrowed it from the website of a group in schism with the Catholic Church and thus not in full communion, so beware of a very strong bias that will be present!).

The main point I wanted to offer that this line of thinking (to which you ask…”really?”) does not come from Trent itself, but goes at least as far back as St. Thomas Aquinas who writes almost the exact same thing in his Summa (IIIa, q74, a. 3). But please note that the Church by no means places her insistence on using wheat bread for the Eucharist above the pastoral needs of her members! The Eucharist is the very heart of the Church, the source of its unity, its source of life. All Seven Sacraments are intertwined with it: Baptism prepares the way to Eucharistic Communion, Confirmation seals and inflames it, Reconciliation heals what is broken and cleanses anew, Anointing of the Sick often prepares one for not merely the reception of the Eucharist and thus a sacramental but nevertheless real communion with Christ but does so here in preparation for eternal communion in Heaven. Marriage mirrors in human relationship the reality of Christ and the Church which also is mirrored beautifully in the Eucharist where Christ–become the bread and wine we consume–becomes one with His Bride, the Church, though the very bodies and souls of all her millions of members. Holy Orders is a sacrament that serves the Eucharist and exists to continue Christ’s sacramental ministry of Himself to all His people, but most especially the Sacrament of His Body and Blood. 
Thus to change the Eucharist in any way is to effect the others as well, for all the other six point to and are bound to it. Has the Church the right to use anything other than water for Baptism? Oil for Confirmation or Anointing? Can Matrimony be ministered to two men, two women, a human and an animal, a child? Some argue today that for pastoral concerns as well the “matter” of the Sacraments ought to be allowed some flexibility, especially regarding Marriage and Holy Orders. But Christ instituted His priesthood, the Church has held since, at the Last Supper when He commissioned those men gathered at table with Him, “Do this in remembrance of me,” and also He charged them with authority over demons, sin, etc. at other points. Holy Thursday has been for ages celebrated not only as the memorial of the Last Supper but also as the Institution of two Sacraments: Eucharist and Ordained Priesthood. This is the way He ordained it; the Church has no authority to alter the Sacraments but rather has the solemn responsibility to preserve them faithfully and minister them to the people of God, without one being given the higher place over the other since to neglect to safeguard them would be to minister nothing to His people, and to withhold the Sacraments would be a great offense to Christ, who came to give Himself to all; that is one river you do NOT want to dam! All the above to say that we preserve and hold fast to the tradition of using wheat bread not simply for the sake of tradition, but because that is how the Sacrament was instituted by Christ. That is what was witnessed by the Apostles, that is what they taught to those would would join them and later succeed them in the priesthood and episcopacy, and that is what has been handed down to the Church today. Were it not a serious issue–and as you say later, if gluten allergies and the like are not new but rather are now better understood–then why would it have been preserved not merely by momentum and keeping the status quo, but very intentionally? Even Aquinas in his Summa again mentions that there were those who used cheese, and still others who would mix a tiny amount of blood from infants in with the flour used to make the unleavened bread! Whatever their reasons, they were condemned as heretics and their practices objected to. After all, remember the parables Jesus would tell about servants who were rewarded for being faithful in “small matters!”

To your next paragraph or so I only wanted to confirm that yes, when on receives the Eucharist under the species of bread or wine only they do receive Christ in His fullness and not in part, though many parishes offer the Eucharist under bread alone during daily Mass, reserving the offering of wine to the whole congregation on Sunday Masses, solemnities and certain feast days. 
To your section on Scripture you are correct; the Greek word used for “bread” is a very general one. But within its contexts (unless specifically noted such as when John specifies loaves of barley bread at the feeding of five thousand) it almost always refers to wheat bread, which would have been the most common kind of bread by far; Aquinas notes also in his Summa the commonality of wheat bread throughout the known world at the time, saying that other kinds of grains are normally used when the wheat crop fails; otherwise rarely for bread at all. He notes also that where wheat is not to be found, wheat specifically for the making of break for the Eucharist can be transported, and throughout the centuries it sometimes was. I should note here that I’m not trying to use Aquinas as an authority on the matter (since as a Baptist I don’t think you would recognize him as such) but more so as a historical witness who was very familiar with the history of such things throughout the ages of the Church and throughout the world at the time. 
To your conclusions:
-Regarding Christ’s use of wheat bread at Passover: No argument here! After all God is very specific in Exodus 29:2 when He establishes the FIRST Passover, saying that they must be made of wheaten flour. However you ought to know that the Church has held since the Last Supper that the Eucharist we celebrate is the New Passover instituted by God who, taking flesh, became the new Moses (i.e. the new law-giver) and inaugurated a New Exodus, giving His very flesh as the new manna for His people to eat along the way. A fascinating, Scriptural and all-around good read on this topic would be “Jesus and the Jewish Roots of the Eucharist.” The Mass is not merely a commemoration or a re-enactment of the Last Supper; it is the fulfillment of the Passover. Christ retained many elements of the Passover but altered a few things: for example, where was the all-important Lamb? As John the Baptist said, pointing to Christ, “Behold, the Lamb of God!” And that same Christ held up the bread and said it is His Body; thus the Unleavened Bread and the Lamb are now one-in-the-same. Just as those celebrating the original Passover had to eat the flesh of the lamb or else forfeit their part in the covenant and God’s favor and protection, so Christ warns that “unless you eat my flesh and drink my blood, you have no life within you” (John 6:53). Likewise He asks us to commemorate the third of four cups–the Blessing Cup–and so we drink only from this cup and not two previous to it, and not one more afterwards (the one Christ did not drink from until just before He died (John 19:29:30). I say all this to try and show how retaining the exclusive use of wheat bread for the Eucharist is in keeping with the Passover tradition we inherited, an “ordinance” given by God Himself to Moses and the people of Israel. Would you have aimed your pastoral critique of this practice against those Orthodox Jews today who insist on the same, for the same?
-Regarding Jesus not specifying “do this” to mean “and always in a Passover fashion:” Then why would He say “do this” during a certain part of a highly-ritualized meal (the Passover seder) and why only with the wine? If this is the interpretation you are taking, then we needn’t use bread of any kind at communion at all, since He did not say “do this” while He held up the bread; only the wine. We cannot remove His command to “do this” from within the context of the whole event–the Passover meal–in which it took place! Also, as I mentioned before, if He did not intend for His followers to “do this” in Passover fashion, why has the Catholic Church and by virtue of them the Orthodox Churches, preserved exactly that tradition all this time from the Last Supper to the Mass I partook in this morning? Even more importantly why have so many Christians during that time given their lives–often in awful ways–in witness to its importance? To disregard the Passover manner of the Eucharist is to disregard their witness (from which the word martyr comes) completely.
-Regarding alcoholic wine: yep, fermented. Often it was so strong they had to mix it with water.
-Regarding “fruit of the vine” and His later refusal of such “fruit” on the Cross: yes, but recall that just before He dies in John’s account, He does accept some common wine. Church Fathers and others have pointed out that in His celebration of the Passover He drinks only three of the four cups, forsaking the fourth until the whole Passover–His passion and death–is completed. The drinking of wine on the Cross completes His passion, the Passover sacrifice of the Paschal Lamb; again the book I mentioned covers this beautifully.
-Regarding Paul’s talk of the Eucharistic Meal being a real meal and not merely a few morsels: many historians agree that originally the Eucharist was celebrated in the context of a larger banquet-type meal, where at some point an apostle or someone duly-appointed/annointed would recount the Last Supper and offer the bread and wine for consecration and such, and from this morsels and sips of the Eucharistic Bread and Wine would be offered to all present. Hence, I would say, Paul’s rant against reducing the Eucharist to simply a matter of eating and drinking: if each is offered only a precious morsel or a sip, the Sacrament retains its precious dignity. If everyone receives a chalice of wine and a hunk of bread, well, that just seems off to me, especially since the Apostles at the Last Supper, during the part of the seder when Jesus would have broken bread and offered the Blessing Cup, would have received but a morsel and a sip as well.
-Regarding Paul, Gentiles and leavened vs. unleavened bread: I believe that since Paul was a very devout Jew (though, obviously, he’d loosened up a bit!) and since he was so keen and careful to “pass on what had been handed on to him), there is a very good chance that the bread they used was unleavened bread though, you are right, it isn’t necessarily so. In the Catholic Church both are found, depending upon the tradition of the particular rite. In the Roman rite, which inherits its liturgical traditions from the Church in Rome founded by Peter and Paul, we use unleavened bread, and so does the Maronite Rite which was heavily influenced by Roman Christians, and perhaps other rites do as well (there are many I’ve not experienced yet!). Byzantine Catholics, who inherited their liturgical traditions from Greek-speaking Churches founded by Paul and his followers, Ukrainian and Ruthenian Catholics (who inherit theirs from the same) and many other Eastern Rites use leavened bread. However, it would be invalid for a Roman rite priest to attempt to consecrate leavened bread, and vice-versa for Eastern Rite priests. Aquinas writes beautifully: “The Roman Church offers unleavened bread because our Lord took flesh without union of the sexes; but the Greek Churches offer leavened bread because the Word of the Father was clothed with flesh, as leaven is mixed with the flour.” Neither point of view is incorrect or even more correct than the other. But the tradition belonging to the particular rite is highly respected.
-Regarding the word “bread” being very general: I think I already touched on it above, but again yes the word itself is general, but often in its context is being used to refer to wheat bread, as it was most common among the Jewish people and especially in ritual/religious instances. As a Catholic I would also add that while almost every reference to bread in the New Testament uses the general word and thus, using a “sola scriptura” approach one could interpret that as a carte blanche to use whatever bread is convenient or pastoral, the Catholic Church is not “sola scriptura” but Sacred Scripture and Sacred Tradition together.

This point–that the Church does not operate on a “scripture alone” basis–touches on your next paragraph regarding Jesus and Paul’s non-specificity as to the exact ingredients of bread used for the Eucharist (even though we know without a doubt that Jesus instituted the Eucharist using wheat, which would have been what Paul “received” as well), in that where Scripture fails to offer instruction or guidance, Sacred Tradition teaches us, and as I have tried to illustrate above our Tradition informs us that using wheat bread was not only retained all this time but also promoted, guarded and extra measures taken to ensure its use, even transporting wheat to remote areas solely for use for the making of altar bread. Yes, a scripture-only approach can yield absurd results (though Jews in the diaspora who celebrating Passover certainly didn’t care where their wheat for bread came from, so long as it was wheat!) but with Tradition reinforcing and illuminating it–and vice versa–we avoid such absurdities. 
By the way, sacramental wine used in the Catholic and Orthodox Churches actually do have strict guidelines regarding sulfites, sweeteners and the like.
Paludanus is a pretty obscure figure (I’d never heard of him before your post!), but in spite of this though he was a theologian and probably taught many people, he did not have teaching authority in the Church; he hasn’t the authority to change a Sacrament! So while in his theological musings he may have expressed a belief that the Eucharist need not necessarily be wheat, that is his opinion on the matter; the belief and tradition of the Church far outweighs this. As for Cajetan, well, there are a couple of them so I’m not sure which one you mean! But again, whether it was the cardinal or the saint (or someone else for that matter) their opinion alone doesn’t undo all that I’ve tried to articulate above which, again, is based solely on history, tradition and theology. As for the claim that Aquinas authorized some other grain (maybe you meant “spelt?”), I can’t find that anywhere. The closest I come is in his second objection in the section I quoted above, where he cites the argument that there are other grains that are very similar to wheat that could be used in places where wheat is scarce. But in his reply to that objection Aquinas says that similarity to wheat is not the same as wheat (elsewhere he defends the importance of using wheat, citing especially the fact that it was what Christ used at the First Eucharist), just as a dog and a wolf, while appearing similar, are not the same.
You bring up again the unleavened/leavened issue in your next paragraph, which I already mentioned. Yet this was a reality already recognized widely in the Church, as I even provided the example Aquinas gave in his Summa, which predates the 1439 declaration by nearly 200 years. As I tried to articulate as well it isn’t that unleavened/leavened doesn’t matter at all, but rather that it matters according to the tradition of a particular rite, and within each rite it matters for a different reason, of which none is better than another but all are equally good and correct. 
Within the decree itself, however, the matter is touched on, as you say, but in the following ways (as borrowed from here- http://www.ewtn.com/library/councils/florence.htm):
“Also, the body of Christ is truly confected in both unleavened and leavened wheat bread, and priests should confect the body of Christ in either, that is, each priest according to the custom of his western or eastern church.” (This is what I said Aquinas said)
“Seventhly, the decree of union concluded with the Greeks, which was promulgated earlier in this sacred council, recording how the holy Spirit proceeds eternally from the Father and the Son, and that the phrase and the Son was licitly and reasonably added to the creed of Constantinople. Also that the body of the Lord is effected in leavened or unleavened wheat bread; and what is to be believed about the pains of purgatory and hell, about the life of the blessed and about suffrages offered for the dead. In addition, about the plenitude of power of the apostolic see given by Christ to blessed Peter and his successors, . . . . . about the order of the patriarchal sees.”
Really the Church was saying nothing new at all in this Decree but merely restating and clarifying what it already believed, to reassure those it sought to reunite with that the Catholic Church was not about to do away with that important aspect of their liturgical life.
Regarding your conclusion (the sentence in bold lettering) I agree with your conclusion in that from a purely Scriptural perspective, disregarding history and tradition and the deeper connections between the Eucharist and the Passover, one could arrive at precisely that understanding. Of course, I disagree with your conclusion personally. And you basically say the same thing in parenthesis following! However, as you can see from all the above, I and many others who believe in transubstantiation would have problems with substitutions, contrary to your thought. At least, I should say, those who believe in transubstantiation and understand their belief to a good degree; many believe in it without understanding, which is fine but makes it difficult to engage in any apologetic defense of their belief, of course. And yes we serve a God who can make one thing into another, yet for Catholics it is about more than that: it is about fidelity to “receive what has been given to us” not only in spirit but in truth, being faithful in matters both small and great and seeking to do so–especially when things get difficult–with great love. It is about more than keeping the status quo or “not fixing what isn’t broken.” It’s about being faithful, as the apostles were faithful, as the martyrs and all the Catholic Christians before us (and before all the Orthodox and even Protestants before they broke from Catholicism), not to honor them but to honor Christ and to trust that if He asked us to “do this” and demonstrated it to us in a certain way, He likely had His reasons.
With all that, then, I would say that the tradition is *not* broken, both in the sense that the practice has been retained and that the tradition of being attentive to the needs of all and serving the least has not been lost either.
The Congregation for the Doctrine of the Faith would not have bothered to issue that letter to the bishops of the Church if a pastoral concern for those with gluten allergies and the like was not a genuine concern. But the Church cannot act solely upon a pastoral concern, nor solely upon a theological or moral concern; she seeks to act in a truly catholic manner, finding the balance that grants the fullest solution, even if that solution involves a measure of sacrifice for the sake of serving and protecting the truth. Permitting low-gluten hosts allows for those with light-to-moderate gluten allergies to partake of the species of bread while permitting the bread for consecration to remain, truly, wheat bread (since all wheat, by its very nature, has gluten in it). This is the balance between saying that those with allergies should partake only of the wine (a completely insensitive response) and saying that non-wheat bread may be used (breaking with tradition and all manner of other things). Thus in using low-gluten hosts the Church is being as faithful as possible in all regards, especially in guarding faithfully “what was handed on to her.” 
My mother is somewhat gluten intolerant, and though gluten makes her sick to her stomach to a degree she loves the Eucharist more than she hates that discomfort, so she offers that discomfort in her flesh as a sacrifice, that her soul may receive nourishment. Most people I have met in the Church are the same way, and those few I’ve encountered who have a more severe reaction to gluten are not only satisfied partaking only in the Cup, but are so grateful to receive Christ’s Body, Blood, Soul and Divinity no matter how He comes to them. I even have met a few priests with gluten allergies, and they offer up their discomfort and pain as a sacrifice as well. For those who have allergies and the like who cannot, because of them, partake of either species, this does not exclude them from Communion nor from receiving the fullness of Christ; at least not in my understanding. There is a spiritual communion that one can participate in, since withholding one’s participation for the sake of one’s health still honors the reality of the Sacrament at least as much as consuming the Sacrament does. I think, for example, of those in the Church who are divorced and, in spite of Christ’s teaching on the matter, remarried and yet attend Mass weekly though they abstain from receiving the Eucharist. Their love for the Eucharist, for Christ and His Church is not necessarily less; though they have chosen against His teaching in one regard the fact that they yet testify to the reality of the Blessed Sacrament and all it stands for is just as powerful as a person in good moral standing consuming the Eucharist. Again, those who cannot receive one or either, in embracing their Cross, can still share very intimately in the Eucharist and in no lesser way than anyone else, if they are willing to endure the suffering of not being able to receive as everyone else receives. Were I to meet such a person I think I would weep; my faith would seem very small in comparison. I don’t think I could endure such a trial easily. But the Church does not have the authority–even if she has the intense desire–to change something like this solely for a pastoral purpose, just as she cannot do likewise regarding any of the other Sacraments. “This teaching is hard; who can accept it?” 
Finally you might find it interesting that God, regarding David and his men eating the shewbread, was not bending the rules at all but was rather bringing out from the depths of obscurity a right and tradition that existed long before the Levitical priesthood: the priesthood of Melchizedek. Note in that passage of the Bible (1 Samuel 21:3-6 and thereabouts) that the priest says he has the shewbread, but the men can eat it “only if they’ve abstained from women.” It was the custom of priests who were performing their duties regarding the Tabernacle and such, to enter into a period of sexual abstinence. The only other customary time when a man might enter into a similar period of sexual abstinence was when they were out on a military campaign (which David and his men were). However, we also must remember that David was a priest, even though he was not a Levite but rather of the tribe of Judah. He wore the “linen ephod” which only priests wore and offered priestly sacrifices at the altar (2 Samuel 6:14-17), and even his sons were priests (2 Samuel 8:18). He was the king of Jerusalem; the first person referred to as a priest in the Bible was Melchizedek, the king of Salem. All men of God’s people were priests in that time; that privilege was lost when the people of God worshiped the Golden Calf, and thus God instituted an exclusive priesthood. Since David was not only ritually pure (having abstained) and since he was a priest not according to the Levitical priesthood but rather the order of Melchizedek (Psalm 110:4), he had every right to eat the shewbread without God having to make any special exceptions at all. 

Now looking at my very long response to your blog, I feel somewhat ashamed at burdening you with so much! I hope, if anything, it expresses not only my love for Christ, His Church and the Blessed Sacrament, but also my desire to help you better understand the Catholic perspective on the issue, if nothing else that the Church may not come across as simply being pastorally insensitive and excluding people from the dearest treasure we have. That is not the Church’s intention or desire at all! There is far more involved than simply what the Eucharist is made of; the extent of things goes far beyond that but all of it is rooted in the Church’s love for Christ and her fidelity to Him. The letter you cited, as well as any other efforts made regarding the same issue, I should hope it evidence of trying to remain faithful still while also tending to His flock as best they can. 
God bless; thank you for such a well-articulated and thought-out post. I hope my response proves interesting and helpful, though please feel no obligation to do anything with it if you haven’t the time or the desire.
-Jacob