Right, time for an update. Firstly...it lives!
But just as I thought things were going to get easier, they didn't for the following reasons:
1) The control cavity needed to be made bigger. I actually bought a SSS strat body template and compared.
2) The pickup cavities needed to be made 1mm wider.
3) The pickup cavities needed routing out to allow for the depth of the screws (the screws couldn't be shortened enough)
4) The neck pocket had to be shimmed with a 2mm piece of sapele veneer so that I could fit the scratchplace under the fingerboard extension.
Any how. The neck, pickups and bridge were all aligned. I changed the pickguard from HSH to HH because the pickguard fitted better and the electronics were simpler to get sorted. The pickups are an old set of PRS Mira (non coil tap). It plays really well although a couple of the frets have been knocked at some point and won't level so I'll need to replace them. But apart from that, the Mira pickups are giving off AC/DC vibes, plus both the string tension and action are satisfyingly low.
It's my first unsupervised build and it's not as bad as it could have been. I'm fairly sure none of the issues would have happened with Fender licensed parts and they would have sunk anyone with just a screwdriver and hex key set. But I managed to solve all the cavity and neck heel problems and come out with admittedly a cosmetically rough but still very giggable instrument. I might just need to start making my own bodies after the next build - tone chasing Phil Collen.