I guess you wanna be real careful left to right on the placement, you should probably string up both E's, get the scale length right (with the intonation screws about the halfway point, just to be cautious? You don't want to find out you drilled it 2 mm too far back to intonate the high E or vice versa). Then you could get the left-right spot just right, mark it, and start drilling. Assuming you want some kind of strat-style hardtail that doesn't sound too hard. If you're using a string-through body hardtail bridge, you definitely want to use a drill press for those holes because they need to be dead straight through the body. A surface-mount bigsby might look cool on a mustang, but other trem options may be too tough.
I like this trend of people cutting up their W bodies themselves - it's inspirational (ie, gives me GAS).