Larger throttle body, larger intake and exhaust valves and more aggressive camshaft.
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Actually the exhaust valves are the same size, only the intake is +1mm.
Heres a good list as to why it makes more power:
Increased intake flow:
Intake valve + 1 mm oversize
Intake cam High lift lobe with 0.9 mm more lift and 12 degrees more duration
Throttle body increased from 60-64mm
Radius on some intake pipes increased from 70-80mm
Increased exhaust flow
Exhaust Head pipe increased frm 60-65mm
Higher flow catalytic converter
Main (single) exhaust pipe increased from 54-57mm
Rear (twin) pipes increased in diameter from 42.5 to 45mm
Block improvements:
Additional air passages in crankcase for reduced pumping losses
Other:
Stronger conrods
New crankshaft with more counterbalance weight
Revised pistons with more valve-piston clearance
Cams:
The exhaust cam is bigger on the primaries and secondary lobes than any other Honda made K series cam. The intake has larger primary lobes than any other K series Honda cam and a type R secondary lobe. If you have to use Honda cams, use 06 TSX cams.
This is also the reason why I keep telling people not to run an ECU from an 04-05 on an 06-08 without it being tuned. There different enough to make a substantial gain in power.