its in the broken down car on the east side of trapper town, you have to go underground to get to the other side, when you get to the other side just "use" the car and you will pick it up
Well, that's how to get the fuel cell regulator. The controller is in Gecko. You must give Skeeter (the ghoul in the junkyard) a super-tool kit for the thing. Or you can just shoot him and take it.
I generally don't worry about the Fuel Cell Controller or the Regulator. Just a waste of time from my perspective, by the time I use all the cars power, I usually have Microfusion cells galore.