Here you see the new K&N filter element snugggled up against the backing plate with the filter pleats skirting around the vent pipe. If you worry about a small air leak under the edge of the element where the pleats are cut you could put a small dab of grease there to seal the convoluted edge against the back plate.

There is another approach to this problem. Rather than cutting the filter element to clear the vent tube you could relocate the tube to clear the filter element. I would start with another backing plate, one from the rear air cleaner without the vent pipe, then cut a new hole and braze in a new vent pipe in the desired location. This should be located about 1/2" farther from the edge of the back plate, and also about 1/2" lower to clear the screw flange on the carburetor dashpot. Do pay attention to the orientation of the back plate. Those vent holes near the center throat go on top.