Still waiting for the final parts... but...
It seems there might be an issue with the power section.
It would seem that current leak from 12/5V into the 3.3V and more or less turn on the circuit even if there's just a single voltage lane (that should be off) active. It could also be that the debug ChipKit I am using, an old broken one, could be outputting current on the power status connection (which will be an input later) enough to open the gate.
As always with electric and digital troubleshooting, the hardest part is usually finding the error. In this case, most likely a well placed diode will remedy the issue. I will look into this tomorrow, but I'm pretty sure it's a minor detail.
On a side note -
I'm certain the end result will be worth it, and there's really no other way to do it properly than to remove all the old "gunk" and re-do it piece by piece. Properly.
So close, almost there - only to be torn apart again.
It's a bit scary to dismantle the machine...