I had rotator cuff surgery about 4 years ago. I had similar issues, the docs told me to rest it for 2 weeks then I went back to the gym, still issues, rest it for 4 weeks, went back to the gym, still issues, had an MRI done and discovered a small tear. They went in and fixed it up, also fixed up my shoulder thermal capsular something because they saw something in there that needed fixing. Now I must tell you that it was an extreme tough recovery process but I felt a lot better. One thing I would suggest is that you stay with the rehab process. I started to slack at the end and it still took me a long time to throw a baseball again and I would not say I'm back to 100% but that is only for really awkward motions that are weak. I don't know if it was the rotator cuff or shoulder or the combination that caused most of my issues but it was tough. PM me if you want more info.