I know it has been a long time since the last post on here but I thought I would add my input anyway.
I really hope you decided to go back to physical therapy. Maybe a new PT though. that really is pretty normal to have the pain you were having. They should have been a lot more sensitive to the fact that your incisions were still healing because I know how painful it is to have them pushing on the shoulder. I didn't start rehab until week 5 and it was very painful even for me. Still is, even after 11 months.
The nerve pain is normal. I have nerve pain leading down my hand everyday. Sometimes to my pointer finger and thumb. Sometimes to my pinky. Depends on the nerve. I am hoping that will go away. But I think it happens alot because I even had that before the surgery.
As far as popping and things go, you probably have a lot of scar tissue and that should clear up as you do better in your physical therapy. It takes a long time to break the scar tissue and you will always have some in there. It shouldn't be something to be super concerned about.
Shoulder surgery is extremely painful. I would NEVER wish it upon my worst enemy. Your going to be in a LOT of pain. That's just how it has to be unfortunately. But you can get through it. I'm actually a little jealous of how well you were doing. I had a capsular plication (tightening of the capsule) and was on hardcore narcotics and literally couldn't move an inch for 12 days. Wasn't allowed to move my shoulder at all or take it out of the sling for 6 weeks. What kind of shoulder surgery did you have? Whatever it was, I wish I had that one instead. lol.