From my 97 VW Jetta VR6, to 2001 B5 S4, and now to my 2013 B8 S4 the first thing I do is always port out my stock air box. It seem like all newer cars the air box gets bigger but the intake to allow the air into the box gets smaller. In any case I cut out about 3-4 square inches of the box on the back passenger side of the box. Also on the front side I added about 20 or so 1/4 inch wide holes. While I was in here I check the air filter but it looks like the dealer I bought it from installed as new one as it was extremely clean.
Any difference in power? No not really, but I was mainly doing this to increase the sound of the super charger as this was recommend. I can hear the super charger ever so slightly now, I still need to get a new intake boot to really increase the the sound.