Just as an aside, is your garden-variety MD up-to-date on this?
Some will have the basics....most will not. They're usually pretty far out of their depth with this stuff, but honestly, so is my endocrinologist. He's a bit of a dummy and I have to help him along rather a lot; poor guy.
It's not the best situation when you're dealing with this crap and want a professional to tell you how to fix it, but the best way forward is to read as much as you can from RELIABLE sources (pubmed.gov for example...or google scholar if that's too intimidating) and go in ready to ask a million questions. You have to be your own advocate. It's harder to do here because of the snail's pace that everything moves, but it is doable.
In terms of doing your research, look for literature reviews that summarise the latest research and find them by searching key terms...i.e. IBS, Crohn's disease, Inflammatory Bowel Disease, thyroid dysfunction...you can set google scholar to give you only reviews and only things written in the last 5 years...which will overwhelm you, but again, its about formulating questions not understanding to 100%.