Aero causing headaches?

Are you doing any sort of core workouts?  I found riding on AB got a lot easier for me when I strengthened my core doing this WO.

I don't get headaches, but I do find my neck gets sore.  I would suggest one or all of the following:

Yoga and/or stretching exercises for the neck.  I have to stretch before/after every ride and on a daily basis.
Ease up on your aero-aggressiveness.  Lower your seat a bit or raise your stem.
Check your sleep habits and position.  Maybe a better pillow and sleeping on your back?

I do core exercises but I'll look into your link as well.

I definitely agree that I need to do some specific neck stretching before and after biking. 

Don't know about the headaches, but the neck pain is common riding in aero at first.  Here's a few things that might help:

Try wider pads.
Make sure your position is supported by your bones and not muscles.
Learn to relax your shoulders, neck and back.
Look up more with your eyeballs and less with your neck.

Did you get your bike professionally fit by someone that knew what they were doing?  (unfortunately professional does not equal know what they were doing...)

A bit of soreness in the neck can be expected if you aren't used to riding in aero but if it doesn't go away then maybe want to look at your fit.

No on the fit.  I'm only using a $250 rode bike for now.  I do know that I am too stretched out because of the angle of my arms.  I have moved the seat forward but it's as far as it can go right now.  I will either need to have a different seat post or something to adjust.  I will put some money and effort into it for the winter training period.

It occured to me that I got mild headaches when I first got my sport touring motorcycle.  It's a Yamaha FZ6 which seats you between that of a sport bike and cruiser so you do have to look up a little if you are positioned with your butt further back.  I changed my seating to being more upright and it went away.

I was told at the Bethesda Naval Hospital that I have a compressed disk in my neck so maybe that is part of the problem.  I know that by just rotating my head today I can hear a lot of bizarre grinding noises.  I may have to do a fitting as well as the stretching stuff too but for now I'm going to back off the aero for a little while.  It just sucks because I feel like I can generate more power from that position. 

Oh yeah. I go to the chiropractor more regularly and got a mattress and it helped a ton. Make sure your fit is good too. If you just started riding on them, it takes some time for the muscles to get used to holding your mellon up. I hit a huge hole once while in aero and it took 4-5mos to feel good again from shoulder to head and the chiro took a scan and all those muscles were tighter than...well you get the idea. Anyway, stretch, chiro, electrostim, and working on my posture at all times helped. Now if I can just get my privates to feel better while in the aero for long times.