Great suggestions on this! One thing I haven't read here as a possible cause is your spine. I was having an aweful time with neck pain and realized it was coming from my neck - I have no curve in my neck! I knew that but it never caused me problems until I started biking. Besides holding up my melon, I had the weight of the helmut and glasses too. Now I'm doing simple exercises to put the curve back into my neck so it shouldn't be a problem next summer. And I have a hybrid bike so I sit up a little taller. I couldn't imagine how my neck would feel if my bars were below my seat level.

I also started doing pilates again too to strengthen my core. Every little bit helps and I feel like biking has made me so much more aware of my body and my posture.