Hi Paul. I use a little PVA glue for sticking nuts on. Superglue is fine as long as you only use a little. You only really need the glue there to hold the nut in place with no strings on. It's string tension that mainly holds it in place, so anything that

As Wokkaboy said, it's important that both the bottom of the nut and the wood it's resting on are flat, so they make maximum contact. There will probably be glue traces left from the old one, so you want to remove those first. If you haven't got any nut files to cut the nut slots deeper if necessary, then it's best to sand the bottom of the nut down to get the nut slots lower. This means that it's one of the last things you should do and you need to be able to string the guitar up with all the hardware fixed in place.

So unless you have, or have access to nut files, then I'd leave the nut off until the guitar is 99% complete. For now, I'd either use tape to mask off the nut area to avoid getting any finish in that area, or simply glue the original one back on. Then once all the hardware is on the guitar, just use string tension to keep the nut in place. Then get the neck relief sorted, set the bridge height for the required action, then work on the nut height. You could probably use some feeler gauges to work out by how much you need to lower it by to get the strings just clearing the first fret without buzzing. But once the bulk of the height has been reduced, it's then a question of removing, a gentle sanding and then refitting the nut several times until it's just right. A gap of somewhere around 0.3mm between the string and the 1st fret on the high E and 0.5mm on the low E should be about it.