Dear J:
Sorry to hear about the soreness in your right shoulder. Certainly, your muscle pain might be due to sleeping position. You might try changing positions and seeing if this helps. If it is related to repetitive use of the arm, then increase the frequency of the stretching and breaks at work and see if this helps. I doubt if you have neurogenic amyotrophy as the pain in this syndrome is usually very, very bad and our patients tell us it is worse than childbirth (the females of course). You might want to get an MRI of the C-spine and see if your have foramen outlet problems (the exit site for the nerve). If the problem were bursitis, rest and NSAIDs would have relieved the pain, and it doesn't sound like you have had much relief. Sorry, I am not much help.
Sincerely,
CCF Neuro MD