I've had a very similar issue and it took me forever to find a solution. As per above had shots, did exercises from physios etc nothing really helped for over 8 months. Constant aching and very uncomfortable feeling in the shoulder, especially anything over head or shoulders back in the squat position.
My advice is don't lift anything heavy over head during rehab, No heavy bench press, back squats or anything that involves the stabilising muscles in the shoulder.
What helped me in the beginning was constant stretching, approximately 10-15 times per day of the effected shoulder. Do a google search for shoulder stretches and begin trying them out, as soon as you find one that gives you the pain at the end of your shoulder mobility, It will probably be an over head stretch that mimics the shoulder position of the back squat, use this stretch. Now continue until you find another stretch that gives you pain at the end of your shoulder mobility, you may only find one that hurts and that is good
if you do find another include it in your stretching routine.
Hold each stretch for 2m in total, you can break it down to 30sec rest, 30sec etc. Repeat at least 4-5 times every second day for first week then every day after that.
Once you are comfortable with the stretches and you feel like progress has been made, introduce self massage of the shoulder muscles giving you problems (probably rear delts but could even be muscles of the thoracic spine area.
Let me know if you need further explanation, I'm happy to elaborate.