Allan,
Honestly the best way to get the engine to breath better is to open it up with a CAI, header and an exhaust. The stock header won't be of much help, that thing is way to restrictive.
As for the smog issue...that will be a pain to keep removing the stock/aftermarket unit to get tested. Unfortunatly no one makes a CARB approved header for the car. The only headers that are approved are Honda/Acura headers.
It's not that I don't like Weapon R...it's just they seem to make some really hooky parts. But hey if they are willing to help you out...then by all means GO FOR IT!!

But your right about them experimenting on your car. Be careful of what you let them do and that really applies to anyone that normally deals with Honda/Acuras.
If you need any more help, just let me know!