I'm having a bit of trouble with the sequence of events here:

I have a poplar neck, and have cut and glued the scarf for the headstock, and cut and glued the heel/backstrap. After I shape everything, it'll get a satin 1-step "natural" stain/varnish.

I have an oak fingerboard. I'd like to stain it to get some more contrast between the oak and poplar.

My dilemma is that I'd like to plane or sand the fingerboard and neck after they're glued together to get that nice seamless feel. If you do that after they're finished, you'll destroy the finish. But once they're glued, applying the contrasting stain is next to impossible.

I suspect the answer is, if you really want more color contrast, use a wood with a more contrasting color (rosewood), glue, sand, then finish.

The same question sort of comes up with the frets. When is the best time to cut the slots, and the best time to actually install the frets? It'd be nice to be able the file the fret ends without worrying about scarring up the finish.