Proceeded to install tuners and neck to check everything was how it should be. E peg hole is a couple of mm closer to the nut whilst all others seem to be evenly spaced and properly lined up.

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Top right shot shows just how lucky I was with the headstock shaping as there is not much meat left there at all. Phew, that was a fluke and a bit too close for comfort. Suggest doing this mock build from behind next time to ensure all fits within headstock design shape.