I had same issue with my right shoulder.  Docs said it was partial tear and didn’t want surgery.  So I spent a lot of time on here addressing internal rotation and has improved the majority of my pain symptoms.  It has taken a long time and I am still not 100% but I don’t have much pain.  This was back in 2010.  Nagging injuries are the most frustrating because you never seem to get the answer or fix you want.  I’d start seeing if your a 1 or 0 on internal rotation and start there. 

I do and I can maintain stable shoulder for most movements.  OH kettlebell squats, close grip overhead squats, ring dips not as well.  I’ve been following the site since the project.  I think the biggest problem is lack of internal rot and extension since when doing the low bar back squat I can’t keep the shoulder as far back. as need and therefore can’t produce the best external rot torque and the elbow takes the hit. I ante up daily for 10-20 minutes but early on I focused more on band distraction (it just seemed easier) and less on soft tissue, but now I’m working the tissue more frequently which is helping. I’ve had 32 years of unbalanced movement that I’m recovering and it just takes more time.

I have a similar issue.  However I can wedge myself in tight but my right elbow is taking serious abuse.  I’m switching to high bar squatting to allow the elbow time to heal.