I have elbow tendinitis that seems to flare up due to benching
I stick with overhead press and flies and seem to be ok as far as pain. I don't know if that translates to your shoulder pain, but it's what works for me.
I often wonder if I'm leaving gaps in my lifting because of the bench. I'm by no means a guy who knows much about lifting. I do zercher squats, deadlifts, flies, bent over rows, triceps kick backs and then several resistance band exercises. Sometimes I do dumbbell presses from a bridge on the ground, I don't know what that's called.
I feel like this is good, but I do wonder if the loss of bench leaves gaps.