Have you been checked for any other auto-immune diseases like hashimoto's thyroiditis and celiac sprue? If you have one autoimmune disease, it is quite possible to have more than one. My sister for instance has lupus and hashimotos and is gluten intolerant. To get a good idea of the thyroid issue, you need to test FT3, FT4, RT3, anti-tpo and TgAb. While your at it: test b12 (should be upper 800's), vitamin D [25(OH)D] (should be above 60). More and more info seems to be coming out about the importance of adequate levels of vitamin D in the body. MS patients, for instance show improvement when they raise their vitamin D levels.
Next, have you done any parasite cleanses? From the posts of others on the parasite boards, those little nasties can travel ANYWHERE and cause a multitude of symptoms and problems.