I finally got to the point where I was happy enough with the finish so I've started to put it together. It's not perfect but I realised that I had more chance of making it worse than better if I kept messing with it.

I installed most of the hardware last night, and the pickups are in but I haven't done any of the wiring yet. I strung it up with some old strings that had been removed from a different guitar and used some leads with alligator clips to test it out anyway though, and despite the hum from the bodged wiring it sounded alright.

The neck had a fair amount of back bow, to the point where I couldn't play anything on the lowest three frets even with the action raised up a lot higher than I'd like, so I adjusted the truss rod and it's a lot better now. It looks like I'll be able to get the action low enough - I'll check the neck again tonight and see how it is sitting. The intonation was in the right ballpark as well so it seems that I managed to glue the neck in about the right position. I'll adjust it properly once I get new strings on there.

I have a couple of issues/questions though:
1. Which way do the washers on the tuners go (bump up or down)? I put them in with the bump up but one of the bushings doesn't want to screw in properly.
2. The neck pickup doesn't sit parallel to the strings - it is angled with the coil towards the neck sitting a lot lower than the other coil. The bridge pickup sits roughly parallel with the strings. What's the best way to get the pickups sitting parallel to the strings?