Been doing a bit of research as I plan to modify my engine cover when I get my Twintake and found this:
http://forums.vwvortex.com/showthread.php?3573551-*DIY-how-to-cut-engine-cover-to-fit-with-an-aftermarket-intake
Gives you a good idea on what to cut although you might need to remove more or less depending on your new system