I was going to pull the stock intake system and put a cone filter on the VAF but my only concern is the air pump that routes into the filter box. Since it obviously pulls unmetered air I assume I can just pop a little breather filter over it.

This is for an 87 Turbo II

 

yes. if you go to rx7.com(http://www.rx7.com/store/rx7/fcintake.html) you can get a Bönez Air Pump Filter for $12.00. So it cheap easy and more efficient than the aftermarket cone filters with the air pump tube that attaches directly(IMO).