Oh my goodness don't even get me started on muscle probs. I've been having them for the past 5 years, but mine are becoming more and more painful because I am uninsured and can't get treated until I get my gold card (government insurance in texas) in 6 weeks. Can't wait. but once you get on the right thyroid meds and everything's balanced out, the muscle problems will diminish.I usually suffer muscle weakness/aches in my legs, so just hang in there.
I also have muscle / joint problems. I suffer from stiffness mostly especially in my shoulder. Muscle weakness also is present.
Sounds like common symptoms to me. You'll get better.