Pretty sure I've got it ran proper now - the rear wiring section wasn't in the right spot so I had the grey plug too low - sits nice with it unplugged so I'll have to mess about with the rear and get that ran proper.

That blue wire is a constant 12v feed from the ignition, that will be wired to trigger a constant duty relay which will feed power to all the other relays to power thermos, ecu, wideband, radio etc. Will probably dual (triple?) purpose the ECU, Radio and Wideband all off one relay and individually fuse each circuit, still thinking that through though.
I also cleaned up the window regs, repacked them with grease and chucked them in too, and the door latches are in. The passengers door closes perfectly, the drivers needs adjustment - that was the side that got the new quarter panel. The latch contacts the door as you can see below. Looking at it the door needs to go forward and the back edge of the door needs to come down ever so slightly. Not a huge issue - panel beater wanted it back to check all this stuff anyway after it was mostly back together.
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