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Hi dragonboy,
Sounds like you're having a similar problem to what I had. I just spent the weekend pulling out my air box, kleen air system, and installing a K&N R-0990 and Factory Pro jet kit.
My new setup is running really well, and finally lets me get rid of the kleen air system without any issues. If you really want to get rid of it, I would suggest dropping the $30 on the K&N filter and the $80 on the Factory Pro jet kit.
Before installing the above, I actually fully re-installed my Kleen Air system because the bike ran significantly worse without it. I'll post up the jetting that my bike had prior to the airbox removal in the jetting database, which might shed some light on your problem. I think for some specific jetting and bike setups, you're better off not removing the Kleen Air system.
Cheers,
Owen
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