So I've been getting into the riding thing more and more, trying to make it a standard part of my day. However, when I go for rides for 2 hours my neck really starts to bother me, right at the base of my spine.
It doesn't hurt that much for sub-two hour rides, but I really start to notice it and sometimes have to ride up in a less aerodynamic position to straighten my neck.
Do you were eye glasses? When I am having problems with my contacts, I resort to my normal glasses, however, the way they are designed, you have to put your head up a bit more then if you wear contacts and cycling glasses and I'll get neck pains like your talking about.
Most upper body cycling pain is caused by poor posture on the bike and/or poor core strength. Poor posture usually involves not bending your elbows enough and thus putting excessive pressure on your shoulders, upper back, and hands. The fix is to bend your elbows (and waist) more, though this may require changes to your saddle and handlebar position.
Core strength can be fixed by simple exercises. Look for books in your library or bookstore with "core strength" in the title.