Fretworn's custom ST-1 (12 string)

[Tweaky]

After spending a couple of hours on it this afternoon I'm just starting to realise how long it going to take me to balance the nut height, bridge height and intonation right.

I also know why they had the nut cut for Rickenbacker stringing - the bridge is designed that way too. So I'm just going to aim to get the main strings right and the octave strings will be out intonation wise, but that is part of the charm of 12 strings anyway.

I was going to say, did anybody actually look at your previously posted photos?
Especially the one above...what a mess...Mr Hart [quoting a old Pro Hart commercial]

What happened mate?
You have 2 strings in the low E nut slots, then 3 in the A nut slots , 1 in the D nut slots, G nut slots OK, B nut slots 1 string, 2 strings in the high E nut slots, and one string hanging over the side of the fret board.

IMHO you need to replace that nut, get a nut ruler, and re cut one with the proper spacing.
A Rickenbacker neck is 41mm wide, your neck is 43mm wide, you are wasting 2 valuable mm of your neck width as it's set up at the moment.
With a 12 string, use all the space you can , fingering will be a lot easier once you sort this out.