I've been to the chiropractor a few times since I first posted this question. He's working on moving things back to where they go and gave me some exercise to do to help with the neck. Mainly he told me to do some upper back weight lifting to help support my neck. I might have a bit of a muscle imbalance from too much swimming (front crawl) and was advised to lift to counter act that and help support the neck.

I have also gone back to my bike shop to see about getting fitted. The shop guys determined that the saddle height looked good, my knee was in proper position in relation to the spindle and they raised my bars up as far as they could- with a 40 degree riser stem. They said that they brought everything up, and back,as far as they could without going to some too stupid looking- post extenders or a new fork with super long steerer tube. I'm going to give it a shot- it feels better than it did before- but it's going to be hard to get some super long rides in with the snow coming in. I ride all winter and will get some riding in- just not the really long ones.

They also told me that if this still doesn't work out I should put the bike on CL and start over. My next question is what road bikes come stock with handlebars level - or slightly above- seat height? the only ones I've found so far are the LHT and the Salsa Fargo.

Thanks,
Jon