John -- 
I understand what you are going through.  I did not lose the SCM, but had radiation, chemo and bilateral ND Levels I through V 4 years ago.  My shoulders and neck have become increasingly painful over the last couple of years.  I can do things requiring movement (i.e. I can still play golf at the old level), but fairly often the aching shoulder and neck wake me up at night.  My docs say just a combination of some SAN damage during the ND and radiation fibrosis.  Exercise can help,  but for now, it's Alleve and some stretching.