I crashed my mountainbike in 2006, speared a tree with my shoulder at at high rate of speed, left me with a third degree separated shoulder. My PT rehab'd me with the Total Gym, elastic bands, and isometrics. I took it slow and easy, very committed. I then progressed to pushups which I do to this day. I no longer bench (how much ya bench) but I do plenty of pushups, pullups, squats, and deadlifts. Believe it or not, squats and deadlifts will grow your upper half of your body as much as the lower half, at least in my experience. Good luck and listen to your Physical Therapist, a little sacrafice now to do things right hopefully will get you to where you want to be.
You'll never see the light if you're in someone else's shadow, or said another way, life is like a dog sled team, if you're not the lead dog, the scenery never changes