I'm so sorry to hear that you haven't been able to get a resolution with your diagnosis. I'm sure that being treated for Hashimoto's will turn your situation around quickly, though, and may clear the air to help diagnose anything else that may be complicating things for you.
I am actually not seeing a GI right now at all - I was diagnosed by my family doctor. My main concern is in my post diagnosis treatment, which so far has been nothing (pretty disappointed in my doctor's reponse). I was given two sheets of paper describing my new "diet" and a list of like 20 foods not to eat. After the research that I've done on my own (and with the help of reading this forum!), I'm realizing that this is a much bigger endeavor, and I'm concerned that I may not be doing the right things for my future health. I think I need some type of professional advice and help, but I'm just not sure what I should expect from a family doctor vs. a GI vs. a nutritionist.
Good luck to you Kara - I hope you find some relief soon!