I got the fit to a point that I felt was acceptable, then this happened,

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The end of the tenon proved too high, so when I dry fit the NPUP with it's ring, the EMG's plug points for wiring foul on the pickup unless you wind it up to the point of silliness. Thankfully the NPUP ring will sit flush against the end of the neck so at least I don't have to try and create a rebate for it.

despite the 3 hours worth of test fitting and resounding and squaring off, and general p*ssing about and agonising, i was pleased to find that the marked centrelines on the neck and body actually lined up! Soo rather than wait and agonise some more I decided that pushing on was needed.
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So in about 48 hours, we'll see if I'm a semi luthier, or if I'm a klutz. Cross your fingers guys!