I had to deal with this issue of irregularly drilled hole spacings on my mandolin project, the source of the irregularity being my inability to drill accurate holes by hand. I managed to source some aluminium tube from the local DIY store that was the right inside diameter to go over the tuning keys, and the right outside diameter for the bushes/ferrules. I cut off a short length and cut some crude teeth in the end. Then I put the tuners in place, lubricated the tuner with candlewax (important, otherwise plating at risk) and used a hand drill to enlarge the holes exactly concentric with the tuner.

My headstock is a fairly soft sapele, and I only needed to resharpen the teeth once for all 8 holes. Now if you've got a maple headstock you'll probably need steel tube and much resharpening, but at the very least it ought to give you a really accurate guide to enlarge the holes by hand.