Trek is coming out with a new TCT Carbon bike in an affordable range.
Giant has the TCR/OCR Comp 3 for like ~ 1600 US.
I think Cannondale's Synapse is offered in a 105 kit - so that may also fit your budget.
You have plenty of choices. Just make sure you get fit right..
Comfort comes from the road you take, good pair of shorts, good fit, and good fitness level.
Less stiff? You mean absorb road shock? - Hmm.. Mountain bike, dual suspension w/ slicks...
Road bikes can only absorb so much... know what I mean? There will be a insginficantly slight deviation from an alum bike vs. a carbon bike for the first 30 miles of your ride. By mile 100, comfort is about how well trained your core muscles are & what bike you are on. If you're doing that kind of mileage - then worry about comfort....
Good Luck!
-Peter