Without seeing your serve, I can't comment on technique. I have shoulder issues as well, but I don't attribute them simply to poly strings. I suffer from a muscle imbalance, which is common if you play a lot of tennis and/or only work the "beach muscles." My new therapy routine involves strengthening my shoulder stabilizing muscles in the around my shoulder blade on my back. You too, may need to address this issue with therapy or simply strengthening your back. Only you doctor/physical therapist will be able to tell you that.
Also, some of my shoulder pain was from biceps tendonitis. The tendons from your biceps run up towards you shoulder, and you may experience pain on the front of the shoulder, near the joint.
Softer strings will help with the pain, but if you have either of these issues, you need to get them checked out. I play with poly mains and multi crosses, and I still have some shoulder pain. But ultimately, the pain is the residual effect from an injury/muscle imbalance, not the strings. I hope you are feeling better soon.