I separated my shoulder once and had to deal with phantom pain while I was working on rehabing it to get it strong again. Trying to rehab when your getting pain that could or could not be phantom pain can be kind of scary.

What I did (and I hope some of this info helps) is almost immediately after my injury, I began moving the shoulder around as much as I could sticking to a pain free range of motion. I got yelled at a lot about it at first, but would find out later that my consistently moving the shoulder in the pain free zone and gradually pushing the range of motion contributed a lot to a quicker recovery. Now getting to the pain part. I started working with therapy bands at first and that didn't hurt much at all but as I began to increase the resistance on the bands and eventually graduate to using dumbbells, I really started having to make a lot of judgement calls on what I could and could not do because of the pain that I was feeling during my rehab sessions.

I did not actually go into physical therapy for the injury as I could not afford it with the type of insurance that I was carrying at the time so I self rehabed it at the health club that I was working at during that time. I was fortunate enough to have become friends with the chiropractor that kept his office in our facility and he was helping me with keeping tabs on my progress. I mostly went off of timelines and where the healing process should be at a given time following the injury to use as a guide. Dr. Kay, the chiropractor, told me that there would be pain during the process and that I would have to be able to deal with it.

As I worked through the pain, I gradually gained the ability to tell the difference between legitmate pain and the phantom pain. The phantom pain seemed to be a more general achey kind of pain where the legitimate pain of pushing too hard had a little more of an edge to it. The differences were still kind of subtle, though and I had doubts from time to time. In the end, I made mostly good decisions and successfully rehabed my shoulder back to normal.

I hope this helps a little. If you have any questions, let me know and I'll do my best.