I guessed that's what you meant. I've got the k&n air filter on with pcIII & two bros pipes & it goes just fine without any box mod. The air is rammed in at speed I guess so no need to create any more holes. If you did make holes, where would the air draw come from as its pretty tight between the tank. I understand what you are after, but other than adding a snorkel type ram, I can't see how you could do it with the lack of space.
2008 DL1000 - Two Bros cans, ProTaper Bar, Oxford Grips, PC111, Givi crash bars, MCA screen, bark busters, rad & bash guards.
1977 BMW R100S - SOLD
1984 BMW R80RT - Sold
1984 DR185 - Retired