Upper Back and Scapular Stability Issues

I've been working out with FB steadily since February. I was so incredibly out of shape that it was kind of like starting with a blank canvas for my fitness. I've lost 35lbs (yay!) but had to see a PT last week because of shoulder pain. I do longer workouts (40+ minutes) every other day and alternate lower/upper/abs + HIIT/cardio using weights.

My PT told me that my mid- and upper-back is really, really weak. Mid-traps, upper traps, lats and the inner shoulder muscles (teres major/minor, spinatus muscles, rhomboid, levator etc). He said that basically if those are weak, then all the chest and shoulder work that FB does will just aggravate the shoulder even more.

I've done some research on those muscles and moves that strengthen them, but I can't seem to find any workouts where FB includes those muscles on a regular basis. Some really long upper-body strength workouts with Daniel will touch on one or two moves that works this area, but nothing regular. Has anyone else had trouble with this area? Are there workouts I'm missing that could help me? Or do you just use other types of workouts for it? I vary my FB workouts all the time, so I'm not just focused on limited workouts. It was such a bummer to find out I'm missing a major functional muscle group. Thanks!

--EDITED TO ADD: My PT is fabulous and walking me through bunches of therapeutic exercises until I can get strong enough for actual strength training for my upper back and scapular area. I'm a big fan of understanding what I'm doing so I also did research on strength moves for the area. The PT is just fine.