Hi Monica,
I agree that we all have our own triggers. However, wheat protein is a fairly common trigger because there's a similarity to this protein and thyroid antigens, thus the autoimmune confusion. Wheat protein is in so many different foods because it's inexpensive, and changes in processing have made it a true foreign antigen.
If you were going to experiment with one thing, I'd eliminate gluten first (in wheat, rye, and barley) and I'd also eliminate sugar, especially high fructose corn syrup because of its detrimental effects on immune function.
It would be difficult to find a doctor who would work with you on finding every trigger although some allergen tests like RAST testing would be helpful. It's the kind of thing, though, that with persistence you could make some good deductions with using a rotation diet. Best, elaine