I think I didn't so much mean that the full metaphysical model must be accepted without question. Rather there are certain core facets that are necessitated. If certain aspects of your Catholic belief went away your belief in that particular religion would change (e.g. if you couldn't believe in the Trinity, you wouldn't quite be able to consider yourself a Catholic, I think). As I should have qualified my original statements more, I'll qualify I don't think any religion is a monolithic set of beliefs, I'm quite aware it's rather fluid and flexible as you describe.
I'm also not discounting someone discovering new tenets via that same type of self-investigation.
I'd be quite interested to learn more about such self-questioning, as well as what limitations if any you impose on yourself.
You are quite correct that certain aspects need to be accepted. I'll use your example to describe a little about how I go through the process of self-investigation.
The Trinity is an excellent example of something I have questioned at various points in my life. There isn't the space here to fully detail my whole exploration of the topic, but I have asked questions like, "Assuming there is an all powerful God, how is it possible for this being to be simultaneously in human form? What if this is all just a metaphor and not meant to be taken literally? Given what I know about physics and biology, isn't it possible this Holy Spirit thing is not real?"
Obviously, one can't arrive at conclusive "proof" in the scientific sense for any of the answers to these questions. But as a professional scientist, I find the process of asking them gives me a way to go and look into these specific topics more fully. It satisfies the analytical part of me that is always asking "why?" about everything. For this reason, I don't really put many limits on my line of questioning, since it's important to ferret out the things that are causing me trouble.
Note that I'm also not constantly questioning everything all at once. This is counter-productive since you basically end up at the extreme wondering if everything you observe in the real world is fake and not being able to believe anything, metaphysical or otherwise (it has been a few years since my philosophy courses in college, but I know this is well-traveled ground in philosophy). To put it another way, at several points in my life, I have explored the idea that God may not exist (or that maybe I'm dealing with the "wrong one"). Ultimately, I have made the decision that I believe there is a God. So I don't go back and re-hash that concept every time I want to explore another facet of my faith.
One of the things I have come to appreciate about Catholicism as an adult is that it's internally consistent from a philosophical point of view. There is a rich history of writings by various Catholic philosophers (such as St. Augustine: http://en.wikipedia.org/wiki/Augustine_of_Hippo) on why we believe the things we believe. Furthermore, the Church publishes the Catechism which has extensive citations for the source texts for every facet of the Catholic faith. From the outside, many of the teachings of the Church can seem proscriptive and arbitrary. But when you dig into the details, you find there is a structure to how it all fits together into a coherent and consistent picture. You may have to do a lot of digging and reading to get to all the details, but it's all there.
I'm also not discounting someone discovering new tenets via that same type of self-investigation.
I'd be quite interested to learn more about such self-questioning, as well as what limitations if any you impose on yourself.