Since you apparently got a new drop bar bike, are things like seat height, position etc. as they "should" be.
Even having the seat 1/4" too low can make you noticeably less efficient over distance.

I assume the new bike is the 2012 Specialized CruX Comp Disc Apex??

SKINNIER TIRES!!!!
bikepedia (which is often wrong) states that you have 33?MM tires.
Put on some 25's.