So sorry to hear you are not feeling well. I do not have IC, but regarding the C diff and your diet restrictions--I've had to restrict some foods in my diet in addition to gluten containing foods due to (my interpretation) inflammatory reaction. I've had low WBC counts occasionally which I believe is adding to more susceptibility to infection. I have found The New Yorker, October 22, 2012 article, Germs Are Us, very interesting and helpful (there is reference to C. diff infection, and basically that we are eroding our gut flora and probiotics help maintain it). I have found that the diet restrictions (in addition to gluten) very narrow, but the increased health really negates any difficulty. I truly hope you feel better and wish you a very happy holiday season.
I became hypothyroid after RAI treatment for nonresponsive (propylthiouracil) treatment for Graves disease about thirty years ago. I have had Synthroid replacement since with more or less the same dosage through the years. About one month after starting the gluten-free diet after confirmatory biopsy, my free T4 level escalated to over 40. I subsequently lost excess weight and had my thyroid hormone replacement dose reduced after many many years. Now two years later, my TSH level has finally normalized (0.05 at lowest) and I am within range for thyroid parameters. Long story short. Changing my diet affected my thyroid hormones and it took months/years to stabilize. I can't speak to your Graves symptoms becoming worse after gluten-free diet, but I can say that my removing gluten definitely had an impact on my thyroid hormones, and my symptoms. I've found that reducing stress, listening to my body and those that I trust, have been beneficial to my health. I truly hope you find relief. Be well.