I've also dealt with shoulder pain from bench pressing...back in the day when that's all I did.
I just recently started to get back under the bar and try some things to work around my obviously weak shoulder.
First, I did other shoulder exercises. Military press being the main one. This seemed to help alot and I'd guess that it's because A)it works the muscles of the shoulders in plane that doesn't cause pain, making them stronger, and more importantly B)it really increased the bloodflow to the area. The shoulder joint has a poor blood supply making it a tough bastard to heal in a timely manner. Simply using the shoulder increases that bloodflow and accelerates the healing process.
Next, I started adding in light bench press while experimenting with different grips. A wide grip brought on pain, while a narrow one eased it. I think this is because having a narrow grip makes it easier to keep your elbows tucked in, helping to stabilize the shoulder joint.
The last key that really helped me was trying to bend the bar. By trying to bend the bar towards your feet and parallel to them, your elbows are Forced inward creating a really stable shoulder joint. Keep your shoulder blades pulled back too.