Thanks guys. I've calmed down a bit now. Plus I loosened the strings, slightly loosened the neck screws and there was enough slop in the pocket to move it a little and get them running perfectly true. It's only a little thing, but it was annoying me.
I just have to accept that the first time doing it completely from scratch isn't going to be perfect. I also changed things on the fly. The bridge here is about 2 1/2 cm further back than the original design and it's making it look a little short past the bridge. The mockups earlier in this thread have been properly adjusted, so hopefully Prototype V2 will be more what I see in my head.
I've also learnt that I should have drilled the truss rod access hole at a very slight angle, which would allow a slightly thicker headstock. It's fine funcionaly, but it doesn't look quite right. I'm going to fashion some kind of string retainer bar to pull them down a bit past the nut.
The entire point was to learn a whole bunch of skills so I need to focus on what's gone right. I've just been playing it and it feels really good in my hands and in terms of how I play, it really works well. Contrasted to yesterday at band practice I was playing my Hagstrom, which I do love, but it has the switch in the same place as a Les Paul and I constantly hit it while playing. It both hurts and changes the sound dramatically mid song.
Anyway. Many lessons learnt for version 2. I'll keep going with this but I'm keen to have it done and move on now.