It may be arseways but here's my method before I start making mods.

1. I would measure and mark the centre of the neck at the nut, at the 12th and the heel;

2. I would measure and mark the centre of the heel rout in the body and the trem rout;

3. Then I would check that the neck is centered with the body and the trem rout (to make sure no modifications are needed - there shouldn't)

4. I would mark the centre position of the the bridge then square it up and fit and drill accordingly;

5. I would then put the low and High E tuning pegs in the neck, clamp the neck into place, then to a dry fit with the low and High E strings loaded though the trem. You will then see where to move the neck (there is a nit of wiggle room) so it is positioned so that there is even room all the way along the fretboard with both the low and High E strings.

at that point you will know thats where you want to drill the neck in place.

you can check where the pen dots are positioned at that time or just plug and redrill the whole lot.

I use 6mm tassie oak doweling from the big green shed to plug.

if you do plug and redrill, make sure you use the neck plate to square it up on the back