Brooke,
I have an arthritic shoulder with a degenerative a/c joint, so I feel your pain. Take all things in moderation, this is certainly true with your workouts. Only you know how much pain you can handle, and if it is worth working out. As for me, I do what I need to do, and worship ibupropen as necessary. You may find extensive stretching before you workout will help you. I hope you find the perfect solution!
Mark