Steven - My warmup is typically row 300 meters, dynamic stretching protocol influenced by Catalyst warmup. Lots of focus on shoulder warm up and dynamic flexability. Lots of yoga positions to open shoulder (down dog, childs pose, etc).
I will often incorporate bands (ido portal style) and do internal and external rotations then I do the small circles by my side, out to the side and overhead. I spend some extra time with a band overhead just pulling back on my left side. Depending on what my day is like I will then get people to help me stretch out with various positions. Often times I am lying on my back/stomach and someone is pushing down/up on a bar I hold over my head. I will also get people to help push my shoulders into a wall (as if I were starting a wall slide with some various positions). My forearm will stay bent 45 degrees and I can't move it any closer if I try to setup for a wall slide by myself.
I've gone through the diesel crew protocol twice, done a lot of hanging on bars with various grips and spent a lot of time doing turkish getups and light weight high rep pressing to get back some mass and stability in my shoulder.
I ended my PT about a month ago, but the guy was really good and hit everything pretty hard.
Garrett - the injury happened on a jerk. I haven't had any issues with my kipping pullups and the doc and PT said it was cool to do them. I don't have any pain so I feel comfortable doing it.