Hello and welcome to NeuroTalk! I have Hypothyrodism, too, and take Levothyroxine for it. Although, I wasn't aware that I had it until the doctor told me my blood test revealed it. I didn't have any symptoms that were obvious to me. I do have MS so many of the symptoms you mentioned are ones I have everyday. As I was reading your post I was thinking "MS" but then I saw where that was ruled out. Lots of different conditions mimic MS.
I'm posting the link to the Autoimmune Diseases forum for you in case you haven't visited there already. You might find someone there who can relate to your situation.
http://neurotalk.psychcentral.com/forum44.html
I'm so glad you found us here and happy you joined. You'll meet lots of very nice and caring people here.