This was my initial concern until I took a closer look. The holes will end up above the swingarm and are pretty well protected. We also cut an oval shaped piece of stainless screen and stuck that in the bottom to keep any large stuff from coming into the filter. That was just for added safety though. I was thinking one could easily take two pieces of the screen and place an oiled piece of foam between them for added waterproofing. Just be sure nOT to cut outside of the little nipples in the bottom of the airbox, they hold the filter in place, cut the screen larger so it kind of snaps down and the filter secures it in place too.
If you do this and don't like it, simply buy a new paper filter and you are sealed back up again. You do have to cut the bottom center part out of the air filter too by the way, not the entire bottom though, just the center part.
