The pump drive gear only goes on one way. When you try to set the pump drive gear wrong, the holes are gone. Line up the timing marks as Robyn's diagrams show, or follow the directions in the post you referenced. 6 one, half dozen the other. The first diagram shows the timing marks for setting cam timing. The reason for using the 12 O'clock (crank) and 6 O'clock (cam) is due to precision. If you use 12-12, you can be off by one tooth and may not see it, even when using a straight-edge (it's that close). The second diagram shows the pump drive gear timing. Set the crank-cam timing, rotate the crank 360, then set the pump driven gear timing (12-6, respectively).