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I've got my fretboard almost perfect to the neck. It's flush where the neck would meet the body but, there is a little overhang on the rest of it.
Now I think, because the overhang is so slight, I can take care of it when I am shaping the neck after glueing the fretboard on. But the next step in the book is doing the pearl inlays on the frets, I also have (came with the kit) the stuff to do the small dots on the sides of the freeboard, but they don't tell me when to do those. and if I do those now, will I when taking the overhang out later file them out?
Thanks.
A lot of information but hopefully you'll get what I mean.

I do the side dots way late in the process when the neck and fretboard are fully shaped and the fretboard sanded level. Basically right before I am ready to finish the guitar. At that point I am good knowing that I can center the dot and it will stay centered.