Nick - I dremeled the port window in the cylinder wall to the specs in the wiki, 1mm wider on each side and 3mm lower. The port window on the exterior of the cylinder (where the intake bolts on) I widened to the dimensions of the inside of the 15mm malossi intake, so there would be good flow. The interior of the port (the actual 'passage') I made a smooth transition from the interior shape to the exterior shape.
So, since I obviously don't want to cut through the guide pin, when I hit that metal, just avoid it and let it protrude into the port? Or am I doing something massively wrong if that is happening?