I have a similar issue with long runs, especially on one side of my neck. I know I run with quite high arms. So, I consciously try to drop my shoulders and let my arms go 'floppy' at regular intervals. Best to do it on easy downhills. I also roll my arms/ shoulders a lot - basically just trying to change arm / shoulder position as often as possible. I find the trick is to do these relaxation movements regularly from the START of the run as a preventative measure rather than waiting until a couple of hours in when the pain starts.
