Everyone here has made some very good points. I also wonder about bike fit. I used to have the same issue on my Trek and thought it was just part of riding the bike until I was measured for a second bike and found out the Trek was too big for me. My top tube and stem length were too long for my short torso and I was too stretched out. My search for a bike with a shorter top tube resulted in my ordering a custom Luna which I love. I have no shoulder, neck or hand pain.

Did you get a good fitting when you purchased your bike? If you didn't, I would suggest getting one just to rule out the possibility that your bike is the incorrect size or to make some adjustments to the one you have.