I've had trouble with my right shoulder for years. I work around it by exploring different lift angles and movements when working chest and shoulders. For chest, try flies, both cable and dumbbell. For shoulders, try standing militaries at a 10 degree or so forward angle. Also, try side-laterals.
In all cases, use light weights to explore the effect those movements have on the injuries and on building muscle tissue.
I think i have a tear in the rotator cuff, i went to the doctor and he send me to do some xrays and stuff, i am just lazy to go haha.
