I keep thinking there are two possible K&N filters for use in the airbox. The one I have is a nearly box-like affair that uses hose clamps to fasten it to the Helmholtz resonator cones on the inside of the lid. For this style, you must remove the stock filter brace which is molded to the inside of the lid as well.
The other type is one that simply replaces the flat stock Kawasaki filter. Do not remove the brace if this is the type you have.
If you can move the airbox/battery holder a bit forward, and are still having trouble with the intake boots, a handy trick to soften the rubber up a bit is to remove them completely from the bike, and BOIL then in water for a few minutes. Sounds goofy, but does really work. Don't lose or forget the boot springs.
Edited for clarity.
Voidrider screwed with this post 05-08-2012 at 05:35 PM