Okay, your workouts (as suspected) are very balanced. Very glad to hear your variety and the areas you target are spot on. To many people train only the show muscles and very little of the go muscles. About the only caution I can offer is one of REST! It doesn't sound like you have enough down time. The increase in max pull-ups following your injury was likely due to the increased rest you were getting and the targeting of primary stabilization musculature by the PT. At least I hope they were targeting them.
That said, I have a few more questions. What does your posture look like? Stand comfortably against a wall. Does the back of your head, shoulder blades, butt and heels all touch with the same pressure? I am guessing your head is held in a forward translation. Now, stay against the wall and raise your arms above your head as if to perform a press and lower your elbow down to shoulder level and slightly below. Do the back of your forearms want to list forward?
One more, this one requires another set of eyes. Have someone stand beside you and raise your arms above your head, feet shoulder width apart and perform a squat. Do your arms want to lean forward?
Okay, one more. (I lied the first time) Reach over your head with one arm at a time, as if to scratch down your back. Can you reach the same spot? Now reach up your back, as if you couldn't reach the itch from the top. Are both arms the same/same distance up the back?
Will check back soon for your reply
Hunting the Michigan Thumbs agricultural mecca...farm country bucks taste the best.