The hole goes exactly in the center of the small side of the crank. The nub that the bearing goes on. You machine an 11mm hole and also take 1mm off the face. Then be sure to round it up a little. I'll post a photo of the pinasco instructions at some point.
Yeah honestly the intake pulse hitting a steel wall on the inside of the crank probably isn't the best for flow and eddying but hey, I guess it's something you can't really change with the pinasco case half. There really isn't any amount of modification that would improve that ... That I can think of.