Welcome to our board, rdial.
Two years undiagnosed is harsh. I was only nagging my doctor for about six months — although in retrospect, I know that I had been hyperthyroid about four years previously for a bit of time. Anyway, six months was bad, so my heart goes out to you having been hyperthyroid for two years.
We’re not doctors here. So take whatever opinions are expressed on the board with a large grain of salt.
I have been told by an endocrinologist that once we regain controlled normal levels of thyroid hormone that the muscle begins to return. Whether all of the muscle returns or not, I do not know. It is not strong muscle that returns — we need to go about retraining it, strengthening it. And we need to start with baby steps: if we slam back into exercise we pull muscles and get shin splints and the like. Listen to the muscles when you start your strengthening exercises. For example, in order to do the required number of reps with my biceps, the heaviest “weight” I could use at first was a small paperback book. Things improved rather quickly, but at first my physical therapist told me that I had only about 8% of the strength of my peers.
As for bone, I think it is unlikely that we recoup the bone. But I do not know.