My '07 C&C w/6spd. manual and 3:73 rear took some getting used to as far as shift points and starting out compared to my '99 C&C w/5spd. and 4:10 rear. I did stall mine a few times, but am used to it now and it is a none issue. As far as your engines performance, there has to be something wrong,as the 6. 7 is much more responsive than 5. 9 in my opinion. I've never experienced what you described.
Jim
05 2500 QC SLT 4x4
07 3500 C&C SLT 4x4