You don't need a glassy finish on the wood because of the difficulties of getting the finish to bind, a little bit of barely perceptable roughness provides the key for the stain / paint, sealer / undercoat.

For my builds I have bolted the neck up, taken a centreline and marked it out from there, I do use low tack masking tape ( the blue stuff ) for marking out so I don't finish up having to get these lines off the timber.

Remember when you set the scale length that the route for the bridge pickup is often not quite in the right place and may require some adjustment, the E1 string is the shortest from nut to bridge and the E6 ( the fat one ) the longest and you need adjustment for intonation across all the strings so bear this in mind before cutting and drilling.

For the bridge pickup route, get the bridge place without the PU in place and once that's taken care of check the the PU fits the cavity without bind

Good luck with the build and ask questions as they arise, lots of clever people on here who are more than happy to help