Shoulder Pain at Depth During Squat

I recently changed the bar position on my squats (raising it about 1.5 inches while still maintaining a low bar position.) It felt fine my first few lifts, but gradually I began to feel a pinching pain in the back of my right shoulder at the bottom of the squat (I've attempted to show the area below.) The pain goes away at the top of the squat, but returns as soon as I rack the bar. It was something I could work through at first, but now the pain lingers to a point where press and bench become difficult. Could this be a form issue? I've also been doing a substantial amount of pull-ups lately and I'm wondering if that could be a contributing factor. I'd appreciate any input, thanks!

Attachment 6939
Attachment 6938
Attachment 6940