The trick I used was put the control pod on as best you can and get it in the right position for your feel (don't got too far forward on the throttle side, your brake lever still has to fit under the throttle cables).
Once you have it in place, pull the bottom plate off, the one with the pin. Keep the top in place and don't move it!
Put a dab of water or spit on the pin, then put it back in place. Wherever it touches the bars, you'll now have a dab of water/spit right where you want to drill. Grab a pencil or whatever and mark that spot. Then drill.
This is what I did and it was spot on, both sides. Plus, no movement.
2009 Aprilia Tuono - Ginger
2001 XR650R BRP (Big Red Pig)
2006 Honda 599 - Ex wrecked it :-D
2007 Honda CB900F (sold)
2006 Honda VTX 1300C (sold)