Firstly, I'd say get yourself to a good physio, there's all manner of stuff potentially going on, and you'd need someone to assess your posture and whatnot to sort you out properly.
Anyhoo, it sounds like you've got mouse shoulder!! It's nothing personal, it's tight upper and middle traps, and 'stretching' them out on your bike is what's causing the pain. I'd suggest googling some upper traps/neck stretching exercises, sticking a hot water bottle on it, and getting a significant other to massage it or you could try googling trigger point release for upper traps. Or do all of the above?!
Because you're looking at a muscle group that combines neck and shoulder/arm movements, it's horribly complicated to diagnosis over tinternet, hence why a good physio can really help. I guess my point is, you can treat the symptoms and adjust your riding position, but you're not treating the cause....
Finally, and most importantly, like Dyna says - DO NOT PUT BAR-ENDS ON RISER BARS.
