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If I understand otterhound's question, the fretboard shouldn't be a problem. If the neck is aligned now, it should be afterward.
The screw holes in the back of the neck are the pilot holes for the inserts. They will need to be drilled out a little, but that's no big. The existing holes will guide your bit.
If you are anxious about being plumb while drilling, you can make a little jig out of a piece of 1-by. Drill a plumb hole, the size of your bit, through the 1-by. Push the bit 'til the tip just pokes out, line it up over the existing hole, and drill.
Lay the neck on a towel or something to protect the FB, and keep the neck stable. I'd also put a piece of tape on the bit, as a depth guide, so that you don't have to put any extra MOP dots on the fingerboard to cover your boo boo.
As far as the fretboard goes, I've been trying to get on top of that learning curvature the greater part of my life!
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