I think I understand your questions.
This sounds very similar to a problem I had yesterday trying to install a set of Gotoh vintage tuners. The press in bushing is .346" diameter and the tuner post is .249" diameter. I drilled the holes for the bushings slightly deeper than the length of the bushing, but not all the way through the peghead, and then followed the center of these holes with the smaller diameter bit for the tuning posts. The problem I encountered though was I did not have the correct diameter bit for the bushings - either too tight or too loose. So what I did was go with the smaller diameter bit and then carefully use a deburring bit on my dremel tool to slightly widen the holes so that the bushing would go in without a sledge hammer
You might try using the nearest size drill bit (but smaller than what is called for) and then carefully enlarge the bushing hole in a similar manner as described above (round file, coarse sand paper glued to a dowel rod in a drill press, dremel, etc.). I think the key is to clamp your peghead to your drill press table (providing you have a drill press), drill your bushing hole to the proper depth, then leaving the peghead clamped in place, drill the same hole with the bit that is the same diameter as your tuning machine post. This will help assure that the two holes are on the same center.
Hope this makes sense.