The nut sits a little above the bottom of it's slot, so that will need filing down and then the guitar will need a proper set up. But it is done intonates pretty well considering the nut...and most importantly of all sounds fantastic and I love the feel of the neck.
In interest of completeness: I wired the yellow and white from the neck and bridge to the top and bottom pole on the switch. The two black to the back of the volume pot and then wired the first lug of the pot to the middle pole of the switch.. I think everything else stayed the same as on the seymour duncan diagram.
I might post a final victory picture tomorrow and then this thread can die and we can all get on with our lives.