Personally, I believe alot has to do with each idividual injection pump. Mine (a 4x4 daully) has always been about 25-40 HP less than other rigs same year, setup and mods. I haven't been told by anyone what exactly would cause this.
I have since had the ECM re-flashed by Cummins, no change.
This has been a sore spot on my @$$ for quit some time.
Just to give you numbers (you asked)
my truck 2001 4x4 3500 auto, BD3's, Peirs HX-40, Edge comp, AFE, 4" exhaust..... last dynoed 365rwhp (can't remember torque)
A friend of mine, same year, equivelant mods... ..... 412rwhp.
Imagine my surprise... ... ... ... my truck is 47rwhp less. I'm Like WHAT.
I've been looking all around for a year now, no answers yet.
HTH
George