When you were fitted for your bike was the focus on performance or comfort? There are some easy adjustments to make that can ease neck pain but take away from aerodynamics such as using a stem with a steeper upward angle. Also core strength is very important for good posture, including neck alignment on the bike. If you have access to a TNT coach you should really bring it up with them.
Living life like there's no tomorrow.
http://gorgebikefitter.com/
2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS