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natek,
I think Momaru is spot on. If you've changed to an aftermarket exhaust and/or removed the airbox, then you might as well pull out the kleen air system before you start re-jetting.
If you have a completely stock bike, then I see no reason at all to remove the kleen air system, and doing so may indeed result in problems if you don't adjust your jetting.
When I bought my bike, it already had an aftermarket full exhaust, and had been re-jetted to compensate for that. When I pulled the kleen air system out, the bike ran significantly worse.
I have since pulled the airbox and the kleen air system and fully re-jetted the carbs, and now everything runs just great.
In other words, if you're doing a significant amount of work (mainly removing the airbox) and re-jetting, then you might as well pull it off, if it's on now and your bike is running well with the stock airbox, then it's probably best to leave it alone.
Regards,
Owen
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