Step 10: Drill Some More
To figure out where to drill these holes I temporarily installed some potentiometers, then using tape stencils and the parts to be installed, I figured out the exact position of the hole on the inside of the case. Once I had this in place, I lined up an identical stencil on the outside of the case. The theory here is that the hole on the inside matches the hole on the outside, such that when you drill through, your part should fit in precisely where it needs to be.
I found what works best in this case is if the 1/4" audio jacks are situated between and "above" (when looking down inside the case) the two rows of potentiometers (and also far enough from the edge to account for the lip of the lid). The switch and power jack position are less critical, but should also be situated "above" the potentiometer.
Once all of your tape is in decidedly place, drill your holes.