Welcome to MC!
The peptides you are taking are for GH release and increasing appetite. If GH increases at all, then it does have some effect on normal thyroid production since GH and thyroid affect each other, but typically you wouldn't get a very big increase in GH from these peptides, plus you are already on T3 and T4 which would mitigate any effects to your thyroid. (In no way am I a doctor so you would do well to confirm this on your own.)
For the shoulder issues, it seems to me that you would benefit greatly from some IGF-1 supplementation. Many here have used it to help with the exact same issue, myself included. IGF-1 speeds up healing and helps with chronic injury. The MCAS store sells it so you have a source for it sitting right in front of you.
You also sound like you may have low testosterone, especially if you stopped cold turkey. It also sounds like you live somewhere besides the U.S.