Are your elbows slightly bent when you ride?
Are your neck and shoulders relaxed when you ride?
You may be able to improve comfort by switching to 25mm wide tires. That made a noticeable difference on my 2013 CAAD10.
And yes, the CAAD is a stiff frame with a generally short headtube. You could try to get some time on a same size supersix to see if it feels any different as the basic geometry is the same for both.
Also spend some time riding less hard and see if you feel better. A tired body won't feel good on any bike.