d3adrock, I mean just remove the triangular shaped plastic cover.  Its held in place by one screw.  Once the plastic cover is removed, replace the painted metal cover.  It will provide some weather protection.  With the stock air box, removing the plastic cover and the snorkel will provide a big increase in air flow along with a big increase in noise.  Removing the plastic cover instead of drilling the big hole in the plastic cover will allow restoration to the stock configuration if you are not happy with the results.

Brendan312, the part number for the cylindrical filter is K&N RD-0710.

The side cover doesn't seal the filter to the box, just keeps large debris from clogging the filter, reducing noise, and restricting airflow. Pulled mine off a couple years ago without any issues.