I almost forgot. The sequence of events that keeps things safe is
1. Turn on 12v supply to controller
2. Pre-charge resistor.
3. Close main contactor.
To turn off, I do
1. Open main contactor,
2. Turn off 12v supply to controller.
It probably doesn't matter anymore, since I think I took care of the problem, but I'm only 99% sure. I fried the mosfets a long time ago by closing the contactor before turning on the controller. I highly doubt it could happen now, but you know.