Sore neck from tri bike...

Pilots who transition from cargo aircraft to combat aircraft experience the same thing since they are subjected to greater "G" loads turning rapidly at low altitude in the nimble fighter planes than in their big cargo planes.

You can proactively condition yourself with any number or combination of a series of exercises. My favorite is the upright row and the bent over row with head held in the forward position as if sitting on a bike looking down the road.

The most common behavior surrounding this stimulus is to simply raise your cockpit. That is an exceptable short term, interim solution but it will compromise bike handling by pulling weight off your front wheel and transfering it to your rear wheel. It is possible it may change the aerodynamics of your posture as well.

If you condition yourself with off-the-bike training to maintain a good, powerful position on the bike you'll become like a fighter pilot or aerobatic who conditions themselves to withstand greater "G" load and can perform better in the real world.

It took me about 8-10 weeks before I could sustain a 40k on the bars comfortably without the urge to sit up.

YMMV. 

don't worry about being down in aero the whole 56miles in the HIM, you will alternate between aero and upright to drink/eat.  This will give you short opportunities to rest and then go back to aero.

one thing I did, was get a bit higher arm rest risers, and relieved the stress of the extreme aero just enough to make it way more comfortable. it was only like a 10mm change but it made a huge difference. just an example of some small changes can make a big difference.

Not sure if you're wearing glasses or not. But I found that when I switched from wearing sunglasses that had a thinker rim on the top to something thinner, I didn't have to pick my head up as much to get the same field of view.

And as others have stated, keep at it. The more you do it, the more your neck muscles will get conditioned to the strain.

BTW, 1st post!

Agree that small changes can make a big difference in comfort, but NOT that planning to sit up a lot during HIM is smart remedy.  This means riding an uncomfortable position for 2 1/2-3hrs and losing any aero advantage to do it (sitting up like a parachute to drink/eat).  OP is much better off optimizing position for his body so he can ride in relative comfort for 56mi. 

OP- Here good (although a little dated) article on tri bike fit

http://slowtwitch.com/mainheadings/techctr/bikefit.html

That's 'jackmott' - great position.

CJ