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Also I should mention that for more dense woods (rosewood, ebony, etc), you want to score the joining surface of the fretboard so that the glue has something to key to. This is especially important for oilier woods like rosewood.
Granted, I'm on my first builds, but this is what I did.
I used a forstner bit in my drill press to make recesses in the fretboard for some 1/4" round fret markers. I then clamped the fretboard to the neck and took a small drill bit and used the center punch hole made by the forstner bit and drilled into the neck at the 3, 9, and 15 spots. I then inserted some small pick guard screws. I then sanded everything the way I wanted it, installed the frets, etc, and then I removed the fretboard for finishing... I was doing an ebony stain on the fretboard and a natural finsih on the neck.
After I got it stained and finished with tung oil, I applied glue to the face of the neck and then the back of the fretboard and then screwed the fretboard back on to the neck... perfect realignment.
After the glue dried, I removed the screws and installed the fret markers.
You are going to be a great builder... You've come up with an intuitively elegant way of handling a task that could be so frustrating...
Thanks, Wes... that means a lot.