Injuries

brett Another thought: try moving your saddle a few cm forward on the rails.
I was initially getting big pain in my right arm on the new bike, thinking "shorter stem", "frame too big" etc. My right arm's effectively a bit shorter than my left because of a previous accident so It was stretching massively and that's why the pain ended up there, but that minor adjustment has totally sorted everything out.

if your lower body is totally fine with the bike i won't recommend doing this as it changes the relation between your bum position in relation to the bottom bracket at the same time, which could potentially bring up other issues and possibly make it harder for you to pinpoint where the problem is. i think for shoulder problems it's always better to alter stem/handlebar setup.