Your right. It doesn't make sense that changes in your thyroid levels could be the cause of all this. It sounds like you have been dealing with the tendon issues for longer then the thyroid has been acting up.
I know how frustrating all of this is for you. I have a family member dealing with mystery symptoms at the moment. Because of the strong family history of spondylitis, we were sure that AS was the answer. I am now wondering if our focus on that distracted the doctors from seeing the real problem.
Not knowing the cause can sometimes be more difficult then dealing with a diagnosis - even a serious diagnosis. That is partly why I followed your "Chronicles of Mayo" posts. We have been considering the Mayo option - probably for the same reasons that you did. I mean, they are supposed to be the best. I am sure that it is disappointing that you did not get better answers. (But gratifying to know that you are doing so many things right.)
Best of luck in finding answers...