Over the Christmas NY period I hand sanded the neck heel to fit and managed to get it aligned enough to screw in place. However the problem with hand tools is that they round off edges and corners and the end of the fingerboard had suffered as a result of over enthusiasm. After a few days of feeling frustrated, I had another burst of inspiration and, after setting up the bandsaw/sander, I rounded off the corners. It looked great.
I also disovered that the electronics cavity was too small.
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It feels like if it's not one issue then it's another. Anyway I carefully took a couple of mm off the sides of the pickup routs and enlarged the control cavity a little. Then the HSH pickguard didn't align properly anyway and I double checked with other HSH pickguards and they were all the same. They were all a bit squashed from top to bottom and didn't sit on the bottom horn attractively. So I'm not sure if the body is the issue or multiple pickguards from both Chinese and overseas suppliers, it'll need double checking against Fender licensed products. However the HH pickguard did align a lot better and it's sort of more consistent with a punk/street asthetic anyway so I went with that and applied some stickers...
The pickups are some SD clones by a company called Johnny Eleca. For Chinese knock offs, they're not bad at all but there doesn't seem to be much difference between split and humbucking modes. Just a little more edge to the split mode. Currently I'm still applying glue to the neck heel and fingerboard edge using a scalpel blade to dig out any bubbles before backfilling. Then I'll sand to achieve a fit.