I'm going through my second round of PT for my shoulder. I had to cut it short the first time for money reasons, but also i don't think it was tailored as individually for me.
i think that an important point - i think with how complex the shoulder is, it's important to make sure your therapy is really geared to your specific problem.
i'll give you my current experience:
i'm having a lot more scapula focus now, with very little external rotation. we're just focusing on Y's and T's, with the T's both supinated and pronated. we have to wait for better scapular position and stability before trying to add L's. W's were troublesome because whenever i broke the 90 degree point, my shoulders would come forward as my elbows came back.
in addition, we are slowly developing my serratus. it's tricky because i thought i could do a pushup plus fine, even while i was working on planche progressions, but it turns out that when i try to extend my arm forward, they slide up as well and impinge. apparently my upper traps are constantly tense, and there's an imbalance between them and my serratus. as a result, i thought i had good strength there, but it's turns out i've developed strength in the wrong spot, and now it's biting me in the ass.
now i lay on my back and practice doing a pushup plus with no weight (or a 3# if i want) while trying to keep my humerus from sliding up (i can feel it when it does). the coordination is really hard, but i can feel when i get it right. i also do circles with my hands, because it's harder for me to keep them from sliding up as my hands approach the center line of my body and as they begin to go overhead. the overhead causes the most potential discomfort because if i don't get a good depression of the humerus, it immediately impinges. this is why the exercise that gave me the most discomfort out of any was pullups. doing a chinup instead actually gives me a bit of a buffer to hold my humerus down.
lastly, we've been doing levator scapula stretches to relieve some of my neck strains.
i have no idea if this is your problem as well, but take it as one guy's shoulder story.