Ah, I think we're just taking about the holes for rear-mounted tuners Grover/Klusons etc, The original LP Jr/Special tuners would have been 3-on-a-stick jobs, so the posts would stick straight out from the sides of the headstock with no angling.

The kit holes aren't in a straight line and are slightly too far apart to fit 3-on-a-stick tuners (I did have a look for my GSJ-1), so its really a case of aligning them the best you can, mark the mounting holes and then drilling the holes out. As Bakersdozen said blutack will help keep them in place whilst you mark up.