The skunk2 intake manifold is an exact copy of the ITR manifold but with a bolt pattern intended to be used with a GSR head. There's no point in putting a skunk2 manifold on an ITR motor. Secondly, you MOST DEFINITELY want a 2.5" exhaust system from the collector of the header on back.

I would do this:

intake of choice (AEM CAI, Injen, whatever)
70mm throttle (Spoon, Erick's, etc)
Extrude Hone the intake manifold and port-match it to the 70mm throttle
"Headwork" from Portflow, DPR, one of those places
skunk2 Stage 2 cams
skunk2 valvespring/retainer combo pack
adjustable cam gears of your choice
upgraded timing belt
CTR pistons
Hytech or SMSP full exhaust (header, cat, etc) or if you wanna cheap out you can get a DC JDM 4-1, Carsound 2.5" cat and custom 2.5" exhaust with the muffler of your choice
Convert to OBD-I ECU and Hondata (the base-level s100 system is fine)
DYNO TUNING