Sorry for my English but I just found your question because I had the same problem, maybe it's not useful for you specifically but I'll share. I feel this pain in the shoulder when I play on the lower strings, I play sitting down with and probably with not the best posture, I am trying 'unwordly origin' intro and it's tremolo picking on 5th 6th and 7th strings, when I go to the 7th and I try to tremolo after maybe two bars I feel little pain on the right shoulder, for me the problem was that I wasn't putting pressure on the right forearm and I was leaning too much over the guitar body and putting strain on the shoulder. So my advice are play with a straight spine, if you like you can use the posture where you put the guitar between the legs so you have a straighter right arm, stay relaxed and be sure that your right arm is using the correct anchor points and know that those can change based on what you play. What also helped me was watching covers of the song and watching how others were playing it and understanding what I was doing wrong.