Why don't you try switching to a Parallel Grip on the Pullups, you can also go wide or narrow depending on the pain factor.
I suffer from shoulder pain on almost every vertical pulling I do, but when I do them with a Neutral ( parallel ) grip, it eliminates the pain. On supinated pullups I always use a extra wide grip, and on Neutral pullups I prefer to stick to a narrow grip. Both hit the back on differently so it's a nice idea actually.
I wouldn't recommend that you stop doing Vertical Pulling movements, but you can find what works best for you. Try doing some horizontal pulling first, then the vertical pulling last.