I spent some time this afternoon trying to sort the nut, I managed to detach it without damaging anything, and removed some material from the bottom until it seemed about the right height sitting in the slot with the strings on, I have it glued and clamped now, I will see what it is like tomorrow after work. It seemed to be a bit better before, but until it's glued down I won't be sure.

One other issue I seem to have is the bridge isn't in quite the right spot, it's a bit close to the neck as the low E saddle is wound back almost as far as it will go and is just in the right position, it would be good to have gone a bit further back to see how that affected it as the first fret intonation seemed to improve as I wound it back. The 12th fret intonation seems ok but I might have been able to have gone a touch further without affecting it too much. Maybe down the track I will move the bridge, I will need to plug the holes as it only needs to be shifted a few millimetres, but that shouldn't be a problem. All part of the learning experience I guess. But the main priority is to get it in tune right up and down the neck first.