Kenny, while doing bench pressing, do you arch your back and retract your scapula? This will shorten the bar path and cause less shoulder rotation (along with keeping your elbows tucked in, per Argajag). Place your elbows down below parallel and make sure you have a non-vertical bar path (the top of the movement should be over your shoulders but not the bottom[aim for your nips]).
Rippetoe seems to endorse the overhead press to rehabilitate an injured rotator cuffs. I don't know whether this is good advice, and if there's one exercise that gives me should pain, it's the overhead press.