I got TMJ in the beginning of my illness as well. My mouth would only open so far and if i wanted to open it further it would make a loud pop in my jaw and be uncomfortable.
I haven't had it in a long time now. As for the collagen I was informed this would reverse itself when your adrenals recover.
In the mean time you could try 6,000 mgs of Vitamin C divided up in 4 doses and 6,000 mgs of L-lysine divided up in 4 doses as well as 500 mgs of L-proline. This is suppose to help the collagen. It also cleans the arteries really well, which people need if they have hypothyroidism.