I just got done drilling one side of the intake for injector bungs. I made up a jig (you can see it bolted to the intake) out of angle stock and 3/8" ID tubing. I used the fuel rails to line up the tubing and tack welded everything in place. I then used a 3/8" bit and a hand drill to form the pilot holes, and ground down a 3/4" bit for a 3/8" pilot (I made up a jig to hold my angle grinder on an x-y table to cut down drill bits) and used my drill press for the final holes. Everything seems to be within about 0.030" of where I intended, but I'm probably going to open the holes up a bit more anyways to give some more room for the epoxy, and I can line them up perfectly then. 
