Hi Vanessa,
Have you considered seeing a natural doctor about some of these questions? I am not a doctor (as you know) but it certainly sounds like you've hit the nail on the head when talking about fungus issues and swelling. I wonder if there is a culprit you have not thought of?
Have you read a book called "The Fungus Link"? It seems like you are quite a go getter and maybe you would be up to a round of that diet to help eliminate the culprit by diet. However, I can also recommend NAET as an option before you go to the meds to check out possible allergens you may not have guessed. They can usually assess you pretty well on the first orientation visit. I understand what you are concerned about with the thyroid meds but if you need them, then of course, it may be the best way to get relief. However, you haven't mentioned what your numbers are. How's your TSH and your antibody tests coming out? Perhaps you can first figure out where you stand with that?
Also, remember that hashi's tends to flare up in cycles and you might be swelling from something that happened (food, stress, etc.) even weeks ago! On my main site, on the health tab, it talks about the cycle of the antibody attack: (sorry about the formatting issues)
Patients with Hashimoto's thyroiditis, an autoimmune disorder responsible for most instances of hypothyroidism, do not have constant levels of destructive autoantibodies. Nor do patients with Graves' disease. Like most autoantibodies, these IgG immunoglobulins only last about 120 days. New antibodies are formed at a rate proportional to the immune system's response. How can these patients be expected to thrive on one standard thyroid hormone replaement dose or one dose of anti-thyroid drugs while their immune status is ignored? Furthermore, dying thyroid cells, especially after radioiodine ablation, release thyroid hormone and autoantibodies. This causes transient symptoms of hyperthyroidism, although in some cases these symptoms may persist for longer than one year. No wonder many hypothyroid patients feel hyper one minute and hypo the next.
I think there is a lot to be learned but one thing may be true: A gluten free diet or a strict change of diet may not show it's full effects and long lasting effects for a year or more after one has transformed their diet and lifestlye permanently. That is what I am currently working on but it will be a slow process. I am taking an eCourse on preparing foods the Nourishing Traditions way (soaking grains, sprouting, etc.) hoping over the next few months I will be healing and within a few more months, hopefully see results in my tests but this is of course, speculation. I won't have proof, until I, well, have proof!

I hope you can find relief soon.
Hang in there.
Mo
