I am brand new at this, so I am pretty sure I am the worst one here to try to give advice. I have been watching scientific anglers videos, Basic Fly Casting and Advanced Fly Casting with Doug Swisher. Everything I had read had made me believe that you were not suppose to use your wrist. But in these videos Doug uses what he calls the "micro-second wrist" I am not sure if that will help your shoulder or not. You still have to use your shoulder, but the quick snap of your wrist may take some of the edge off your shoulder. If you would like to try one, just PM me your address, I'll loan it to you. Just send it back when you are done. If I was good at this I'd let you have it, but I still watch them a couple of times a week.
"If we lie to the government, it's called a felony, when they lie to us, it's called politics." Bill Murray