I don't blame you for being confused. Everywhere you look and read there are varying opinions and it's really hard to sort it all out (if not impossible). People get really passionate about their paticular diet or suppliments and what is good for one might not be so for another.
This is what I think and what I personally try to do.
Avoid Soy and any phytoestrogen producing foods (flax). I think our nation is way too heavy on soy additives in many of our foods and this isn't a good thing. I can't get any good info on whether or not the oils from soy and flax are bad or not but most of what I read suggests not.
Avoid Omega 6 (Linoleic acid) as it suppressed thyroid. I hear over and over again that virgin coconut oil is the best for people with thyroid disease.
Avoid goitrogenic foods like raw cruciferous veggies, (again) soy and even things like strawberries, peanuts and spinach. This is a bummer to me because I really like these foods
Get tested for celiac disease because many autoimmune diseases go hand-in-hand. The tests aren't 100% fail safe and if you really think you have a problem go gluten-free for a few months to be sure.
I'm not convinced about the whole candida and yeast thing but that's because I don't have any evidence that it's occurring in me. Others swear by it. I think we all need a balanced diet that includes complex carbohydrates, proteins, and good fats and try to avoid overly processed foods whenever possible. I do my best to keep it simple.