Long night, but I was able to get the 12 volt power supply working properly. I initially wired it up so that it pulled power off the same connection on the primary contactor that the motor controller used. This ended up being problematic as the 12 PSU would siphon off any charge built up in the caps in the motor controller which did three bad things:
1. Drained the caps in the motor controller, and also prevented them from being able to pre-charge, this is bad for the controller.
2. It made the headlight and 12 volt indicators flash on and off as they pulled residual power from the controller, once the key was turned off.
3. This parasitic load on the power system made the charger never reach a "full charge" state.
The easy solution to this problem was to use an extra set of switched wires that were on the key-switch to turn on a relay that turns power on to the 12 volt PSU. Key switch off, motor controller can keep is pre-charge because the PSU is disconnected. Key switch on, primary contactor enables power to the motor controller, second switch poles turns on relay and the 12 volt PSU gets power and the headlight and indicators turn on. Turn to position Labeled "Start" on key-switch and for some reason the second pole is disconnected and you enter a mode that I've dubbed "stealth mode", where the motor controller is on but the 12 volt regulator is off, so no indicators or headlight, perfect for sneaking up on people Ninja style.
I also removed the split loom and replaced it with spiral wire wrapping. This resulted in a night and day difference in the spaghetti factor. I also took the oportunity to cut off a lot of excess cable length, and combine several wires that had individual crimps into single crimp connections.