I am currently in PT for neck/upper back problems, and was told the same thing about sticking to plain cardio and not doing anything with my arms/shoulders. I asked my PT about workouts, yours will be the best to lay out what is right for you, but mine gave me some great tips. Pilates style workouts, mods on other exercises, and the benefits of an exercise ball (now I sit on one at home to help my core!) Definitely talk to your PT, that is what they are there for! Good luck!