The Catholic Church cares about rigorous scientific methodology because theology is a human science that uses reason to articulate and then explore Divine Revelation.

Reason is used to establish if something is divinely revealed. Only then is it appropriate to make an act of faith in it. No contemporary miracle can possibly fall under Divine Revelation, so the only way to determine if some act is miraculous is through some rational process.

Catholicism does need science, metaphysics, ethics, history, and every other field of human knowledge. These other fields do not "need" Catholic theology because they have their own principles that are not dependent on theology.

This is development of doctrine. The doctrine becomes better understood over time. That does not mean it was not believed before that.

In my opinion, you are stretching the concept of development of doctrine past the breaking point. If you want to say transubstantiation was arrived at by development of doctrine, that's fine with me. If you want to say belief in the real presence goes back to the earliest Christians, that's probably supportable. But to say the earliest Christians believed in transubstantiation is beyond anachronistic—it's just wrong. It's like saying Newton believed in General Relativity because he believed in gravity. Einstein just developed the concept of gravity further. But Newton believed in gravity, so he believed in General Relativity.

As everyone knows who has taken part in these kinds of arguments, the Immaculate Conception is now infallibly declared dogma, yet Aquinas argued against it. The Immaculate Conception is a case of development of doctrine. Does this mean it was believed by the earliest Christians? It definitely was not. It would have made no sense to them.

It is just so easy to ignore a passage when you are a protestant pastor.

You said it, man! Those protestant pastors! Sheesh!

Why would he think about it? It is just so easy to ignore a passage when you are a protestant pastor. I know I heard sermon series on John and did bible studies that walked through the book chapter by chapter. They all skipped the last half of chapter 6. Nothing to see here.

I think it's closer to say they fleshed out the doctrine, no pun intended. I think many in the early church believed they were participating in some important way in Calvary and that they were consuming in some way the body/blood of Jesus. However, as you say, it wasn't until later that all the sacramentology developed, much of which seemed unfortunate and left the actual church members out in the cold, again, sometimes literally!

I believe it. The scripture always seems clear when looking back through an interpretive lens and community. I talked to my old pastor friend about the Eucharist and he seemed mildly uninterested, like he'd never really thought about it before!

This is development of doctrine. The doctrine becomes better understood over time. That does not mean it was not believed before that. Language and philosophical categories might be used for the first time but the reality of it was understood in some way since the beginning. I gave you a list of quotes from the church fathers. Shameless Popery has a new post up on the subject yesterday
http://catholicdefense.blogspot.ca/2014/02/did-tertullian-deny-real-presence.html

The basic Catholic understanding of the Eucharist, the one protestants see as idolatry, was taught in scripture and by many of the church fathers.

Of course contemporary scholars have a lot to contribute to our understanding and many valid readings of the Scriptures can exist side by side.

[Y]et *they* are capturing the authentic meaning of the New Testament?

If the authentic meaning of the New Testament has been clearly understood and explicated by the Fathers of the Church and scholars of the past, why is there any point in contemporary scholars reading the New Testament? I have no problem at all with the idea that contemporary scholars may be able to point out misreadings of scripture that have persisted for many centuries. For example:

24 When Pilate saw that he was not succeeding at all, but that a riot was breaking out instead, he took water and washed his hands in the sight of the crowd, saying, “I am innocent of this man’s blood. Look to it yourselves.” 25 And the whole people said in reply, “His blood be upon us and upon our children.”

The interpretation of the Matthew 27:24-25 has changed since I went to Catholic school.

From your linked article:

Many Catholics and non-Catholics alike think that the Roman Catholic Church invented the doctrine of transubstantiation.

Of course the Church invented the doctrine of transubstantiation, just as Einstein invented the Theory of Relativity and Darwin invented the Theory of Evolution. As I said above, real presence and transubstantiation are not synonyms. In a very real sense, the Church invented the notion of the real presence, too. This should be something the most adamant atheist and the most devout Catholic believer should be able to agree on. Transubstantiation is the Church's explanation (or attempt at explanation) of a phenomenon (whether real or not), and as with any church doctrine, it was formulated within the Church and defined as doctrine by the Church. I know the Catholic Church is very much committed to the term transubstantiation, but transubstantiation is couched in Aristotelian philosophy. To insist that a Catholic absolutely must believe in transubstantiation would be to insist that he or she was required to think in Aristotelian terms. I really don't think the Church requires its members to accept all of Aristotelian philosophy or to think that it is the only way to describe reality. If theologians ever come up with an explanation that retains all the meanings and implications of transubstantiation but uses some other philosophical understanding of reality, I don't believe that will be heresy. I think the real presence is a mystery, and transubstantiation is what the Church considers the best available explanation of it. But mysteries cannot be explained, so I do not believe anyone is required to believe transubstantiation is the only way (or even the best way) to understand the mystery of the real presence. On the other hand, there are explanations that have been ruled out (consubstantiation, transignification), so it is not as if Catholics are free to affirm the real presence and subscribe to any explanation they want.

I am, however, not sure why it is really important to believe in any particular theory of the real presence. As I said earlier, the thing about mysteries is that they can't be explained, so I don't understand why one must affirm any particular explanation of a mystery. It seems somewhat arrogant to claim something is a mystery and then claim not only to explain it, but also to require people to accept a particular explanation.