I am sorry to hear about your shoulder and the pain in the arm. First, I think that carpal tunnel is likely the cause of some of your hand pain, but not related to your shoulder injury. It is difficult to explain how a distal median nerve problem, with the EMG findings of carpal tunnel could be from a shoulder injury with no other EMG findings above the wrist in the median distribution but having a generalized distribution. The other symptoms you describe are very compatible with a shoulder injury. I can't tell you how to talk to your neurologist, if the lump is visable and tender, then it has to be recognized. I might suggest seeing another neurologist, a second opinion. Without examining you and seeing the MRI and EMG studies it is difficult to give to reasons for your pain. The EMG does not pick up small fibers and these are the pain fibers so the EMG might not be the test for pain. It might be that you will have to find methods to control the pain as it sounds like this might be be resolved with other methods. Lumps are difficult to assess over the internet and you should know that when a bone heals, there is extra remodeling taking place and this can give rise to a lump. The larger the area of healing and the more times an area has to undergo the healing process, the bigger the remodeling. This may be why your lump is present.
I am sorry that I can't help you more.
CCF Neuro MD