Official Luthiers Forum!

I'm about to jump into my first set neck build. Is it best practice to finish the guitar once the neck is glued or while the body and neck are still separate?

It's done both ways. There are benefits and trade-offs to both approaches.

I have concluded for myself that finishing after the neck is set gives the best results in the best time.
No worries about the cheeks of the heel not matching the body due to finish build, no rebuffing after setting the neck, no worries about keeping finish off the joint surfaces (less masking and no chips from pulling the mask).

_________________
Brian

You never know what you are capable of until you actually try.

https://www.howardguitarsdelaware.com/

Thanks Brian, that confirms some of my initial suspicions. I've only done bolt-on's so far, so I've always just attached a holder onto the end of the neck and into the neck pocket to hang the guitars to dry and give me something to hold on to or hang when I'm painting. What's the best way to accomplish this with what amounts to a complete guitar?

On most set neck guitars the curve of the cutaway(s) blends into the neck heel. If you finish them separately you will not be able to sand them perfectly flush and there will always be a seam between the two parts. You almost never want to take this apart (unlike both an acoustic or a Fender style joint).
So unless you are using different finish materials or colors I would suggest finishing neck on.