I bought a new Cannondale (R-700) last fall, replacing a 12 year old cannondale. I have had a great deal of difficulty getting a proper fit on this bike. I continue to develop pain in the base of my lower neck after an hour on the bike. At first I thought this was just something that would improve, unfortanatly this has not after 800 miles this spring. Did not have this problem before.

I am thinking I am a little stretched out. Any suggustions?

It could be that you're too stretched out, or that your hand position is too low. Getting a professional will be the most likely response. Try turning you stem up (un-flip it) if you haven't already done so.