Be sure to have the bike properly rejetted. I can also vouch for a long line of headaches in trying to get everything perfect. I messed with the jetting, airbox, pipe, head, etc and pulled 200 horses last year on a 1998 CBR.
This year I tried the same thing with a few extra tweeks and knocked everything off line. I'm literally back at first base.
(In reality, if I would get off my butt and actually dyno the bike I would be able to get the torque and horsepower to a reasonable amount, but I always seem to find other things to occupy me. Things such as wife, kids, wife, yardwork, wife, grad classes, wife, work, wife, wife, wife, wife, wife.)
If you have a good, strong running bike I wouldn't worry about the airbox. That is until you have literally done everything else and the motor and carbs literally require and beg for you to mess with it.
If you want to see a big, and I mean big power improvement go with a set of Keihin flatslides. You will lose a lot of the bike's streetability, but it will make it fun.
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