Two things:
1) Is the neck flat?
2) the fretboard probably isn't flat so you can't use that as a guide.
If the neck is not flat, I would personally glue a maple veneer on the neck face and use that as a base to fill any dip and flatten out humps. Also, if the truss rod isn't straight, you might have to replace that as well.
For the veneer, you could add a 1/16" piece, up to 1/8" and run that over a jointer. That way, you'd have a solid surface to work with. That should bring the whole thing level with the rod.... but really, I wonder if all of this effort is really worth it, but I digress.
Another thing: Does the fretboard have a locking nut shelf?