Very nice set up! Is there any reason I couldent have an airbox built to house the filter and use your kit? I.e. clearances with rear shock, swingarm, brake rotor, etc. I have never seen an aftermarket lt500 airbox.

Like mentioned above.  This kit is an airbox delete kit.  Both SBLT and we made this type of kit.  Your best bet would be like Rider414 mentioned in using the Duncan Racing adapter.  This bolts to the OEM airbox and lets you put on an aftermarket filter.

Somebody could design an aftermarket airbox for the Zilla pretty easily I believe.  There should be no shock clearance issues as the OEM carb to filter boot goes around the shock.  You would need to come up with a good design for the air intake though.  I'm assuming you would want to keep water/mud out of the box, but allow enough air into the air box to make some good power. 

Good luck in what ever you decide to do.