This is the way I did it (extended version of this:
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I was really worried about it coming our wrong so I verified myself in multiple ways to be sure. So this has some extra steps that convinced me it was okay to drill holes.
This is before the neck has been installed.
I used
stew macs suggestion for a fender bridge on a 34" scale bass: #0093 Fender® Style Bass Bridge 35" ± 1/16" from nut to center of rear-most mounting screws.
Laid some masking tape down to protect the finish and give me a place to draw lines on, found center of the neck pocket and extended it back to the bridge.
I clamped the neck in the pocket (I used thick rubber pieces to protect fretboard and bass body) and strung up the neck and bridge using some wire in place of the E and G strings.
I also taped down the pickguard and loosely fit the pickups to be sure the pickguard position was correct and the wires we're close to the correct position over the pickups.
With the neck clamped tight in the neck pocket and strings even with both sides of the fretboard I measured 35" from the nut to the bridge rear mounting holes using the tuners to shorten or lengthen the bridge position. By measuring to 35" on both the E and G sides of the bridge I was relatively sure the bridge was square with the neck/neck pocket.
I then checked, rechecked, and rechecked the bridge position and string alignment along the neck many many times. I also drew lines using a straight edge extending the neck along the body all the way to the bridge. This way I could see the bridge was centered with the neck. Once I was happy with the bridge position I drew a line at the front of the bridge and measured from that line to the neck pocket to be double sure the bridge was square with the neck/neck pocket.
I even second guessed my self and broke it down for a day to come back the next day.
Marked the hole centers for the bridge, center drilled and then pre-drilled the holes.
