When I bought my kit the neck came with a standard plastic nut installed but I had Pitbull include a bone nut so that I could change it out for that one. At what point in the guitar building process should I make the switch? While I am sanding and finishing or later on during set up? Also, how can I go about removing the original cleanly and install the new one?
Generally I'd leave it in until very late in the build - carefully score around the edges and you shouldn't damage any finish.
To remove - score, then using a hacksaw, cut in half along the length of the nut (don't need to go all the way through). Grab some pliers and squeeze the two halves together - should break the glue.
To affix - two dots of superglue - don't need much.