How can a 911 3.4 have so much more HP than a 3.2 Boxster S?

[The Radium King]

that is what i am running (except the 996 intake manifold - i just have the 997 plenum) and the full top speed catless exhaust. i found that the 996 tune really opened up the car. i can run with 987.1 caymans on the straights now. how was the fit for the 996 intake manifold - you had to tap the head and add additional bosses yes? i would expect the longer runners would add some torque.