Nice...
when i drilled the neck, i had it in the pocket... used a drill that was a good fit in the body hole to start, just the pointy bit, just to center tip for the hole, and kind of counter sink the neck at the start...
then worked out the depth and put electrical tape as a flag, then more tape around the drill shank to pack out, using the body holes as a jig to get the hole on the neck vertical... or at least aligned and centered to the body holes... and less likely for the drill bit to wander, if the dowl is harder or softer
you got hold of a pillar drill which may help, but may need some sort of rest to keed the neck flat... I used a simple whirrly hand drill to go by feel.
Pics n keep it coming...