I'd run with an Apexi, TRD or K&N panel. Most of the foam ones don't filter that well. In saying that I'm running a TOM'S filter in mine & it's a multi layered foam type but that's only because it was about half the price of a K&N at the time & I'm a bit of a TOM'S whore.
Have a read of this performance air filter test http://www.mkiv.com/...filters_test/2/ & http://www.mkiv.com/...filters_test/1/
This is the valve you need to disconnect the vacuum hose from to keep the flap open. I left the solenoid & lines in place just in case I wanted to revert it back to standard for about a year then last time I was cleaning the MAF sensor & air box I pulled it all out to tidy it up.