Well, I just laid the holes out and drilled them at the same time I drilled the pilot holes for the jacks- it's all a matter of layout. The way I did it was to lay out all the holes (regardless of size), centerpunch them, and then drill them all with a 1/8" bit. I then went back and redrilled the TRS jacks with a 7/16", the MIDI jacks with a 15mm, and the combo jacks with a 3/8" (the pilot hole size for the punch). I always prefer centerpunching and then centerdrilling with a smaller bit before bringing out the heavy metal- it makes the finished result much more accurate...
If you didn't lay them out to start with, you can cheat a bit. Slipfit a jack into each jack hole, and align it so that it is square with the plate (maybe by using a try-square on the edge of the plate and the flat on the back side of the jack, for example). Then, using a fine scriber, you can mark the hole locations on the plate: put the scriber up into the mounting ear, and twirl it a couple of times. If that doesn't leave enough mark to see, and you don't have any Dykem (layout dye), black out the neighborhood of the spot with a magic marker first. Viola', poor man's Dykem! Pull the jack out, centerpunch the marks, and drill them. That ought to work almost as well as laying them out to start with, and will acommodate any slightly sloppy work in making the 15/16" jack holes.
I also drilled out the mounting ears on the jacks to 1/8" so that I could simply mount them with poprivets. I didn't see any reason to go chasing all over the place looking for those dadgum screws... (;-)
