I don't know if it was the bike or not, but it had to be cause now I feel fine. I was riding a Trek Pilot which has a sloping top tube and I always felt kinda crunched up on the bike. I went to Trek a few times for fits and got 3 different one (3 different people) Still had the pain......My husband bought me a Specialized Ruby which has a straighter top tub and different frame geometry, all I had to do was put a shorter stem and got fitted once and the pain went away. One thing you have to do is stretch your neck before, after, and during the ride. Make sure you are not leaning on your handlbars too much, too much weight forward can hurt. Try tipping the nose of your saddle up a teenie bit so that your weight is on your sit bones, and you are not sliding forward.
Also while you are riding shrug your shoulders every few miles to make sure they are not all tensed up. Sounds like you need a real experienced fitter to fit you correctly. Everyone is different. Good luck, but DO NOT give up!