Is it possible to put different factory filters on different factory intake systems?
The Apexi filter (http://www.mkiv.com/techarticles/filters_test/2/index.htm) seems to be one of the better choices for filter performance.
Is there anybody out there that has tried or is currently doing this?

I have dont it with my hondas it works but you may want to check the pipe size and the filter inlet size..it can be done...

Better off just buying a whole new intake.

Has anyone tried out the Apexi universal filter?

most filters will work with other intake tubes. you just want to make sure you get the right opening.

Most intake pipes are made with 3" diameter so any 3" will fit on any other one as long as the filter diameter isn't bigger or something. There are 2.5" piping systems out there too so make sure you measure.

Most all filters now are made with cotton wrapped in mesh like K&N started with so they are all pretty much the same if they are oiled.

All the oiled gauze filters will work about the same on anyone's intake. They will stop low-flying birds and large insects, and that is about it! :)