Pain is your body telling you to stop or alter the routine. As a long-time fitness trainer, it is important to listen to your body. Moreover, consult a physician if tis pain persists.

i stretch gently to work on rotator cuff or deltoid pain in my left shoulder. this is my own apprach. i haven't consulted a physician. if the pain is serious i'd see a doc

First, talk to your doctor....
Are you using weights during your strength training? Maybe try calisthenics only for awhile and slowly build up to weights if there's no medical issues...

Good luck finding an answer. I tore my quadriceps tendon last year. Fortunately, no pain or discomfort. I avoid explosive movements like box jumps to guard against re-injury.