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Long story short, I filed away too much at the base of the channel for my nut and a little too much away from the side by the headstock veneer (because I neglected to cut an angle on that face.) All the faces are finally perfect but the nut is no longer snug and IMO a tad too low and I'd like to make a shim. Is this a common thing to do for a newbie such as myself? Should I use the same woods as I used in the construction of my neck, which is a laminate of mahogany, maple and walnut? If not will it rob the guitar of tone somehow? If anyone else has done this can you describe or show what you did?

Without seeing exactly what you have going on I can't say for sure but I sometimes will shim a nut for height. When I do I use a piece of bone. LMI sells bone shim material that is .030" I think, or you can cut your own at the band saw.

Does it have to be bone? I was hoping to just use wood and epoxy.

I admit i have done this before, and used the same wood as the fretboard, but have always meant to make a new nut. if i had another one at the time I wouldn't have shimmed it;nuts are cheap. I think the bone shim would be a better long term solution..

the more I do this the less I have found that Epoxy is the worse glue we can use.
I rate the wood glues this way
Hot Hide and Fish Glue
Tite bone
Elemers White

Duco Cement
Weld on
Plastic to wood

CA for repairs
be careful as it can bleed into some woods

To ship the nut the best results are not as a shim under the nut but to add to the nut. In case of Bone or Ivory all you need to do is glue a piece on the bottom , here CA will be acceptable. On plastic I use CA or Duco.

Here's a couple of pictures to clarify:

At this point I'd go for a new nut.

Yes you will have to fill that with Mahogany to match the neck. Next time put a stop on the file so you don't go so deep. A good clean fit shim here will be in order. Use fish glue or hide glue to help lessen the glue signature. NO CA.

From The pictures it looks like the top of that blank may be at just about the right height on the center of the board and a bit to file down at the ends. Run your half pencil on it and see what the line looks like. If the small gaps in the woodwork will not keep you up all night, it may very well play as is. If you go that route just glue the nut to the end of the fret board with a couple of drops of white or fish glue.

Neil,
Not to fear. Use any wood you think looks okay and glue it down in your trench. You already the nut sitting on wood (mahogany).! As for the fit front to back, you can take your cut offs from the headstock veneer, make a thin shim that will fit between the end of the veneer and the nut, glue the shim using CA and trim, sand it back to fit and blend....no one will ever see it...same wood and CA will make it blend together lovely.
That is what I would do.

Kevin