One can get the fuel cell controller from Gecko. You need to trade with the mechanic ghoul named Skeeter, who can be found in the Junkyard. He will ask you in dialogue to trade him a super tool kit for the fuel cell controller. Before leaving, however, search for some pliers in Skeeter's workshop. The super tool kit can be obtained from Vic's daughter in Vault City. She resides in the Maintenance Center, and will require a set of pliers and a wrench. This is perhaps the quickest approach; a list of alternative locations can be found on the super tool kit page.
Pliers are easily found throughout the game, and are otherwise a garbage item. Wrenches are harder to find, but can usually be found around mechanics' areas, especially on tool boards. You can receive the location of a Wrench outside Vault City by completing the Mr. Nixon doll sub-quest for the crying child south of the medical clinic, also outside of Vault City. This can be done by finding the doll behind the Spittoon, Cassidy's bar. Then, listen to the child to find the location of a wrench. If you are already a citizen both tools are available in a storage room in the Vault.
Additionally, in Klamath after you have defeated Keeng Ra'at proceed outside and click on the broken down car south of where you come out of the tunnels in the garage. The fuel cell regulator is inside. This item greatly reduces the amount of energy used by your car. Smitty will be more than happy to install either part for you. The fuel cell controller for $2000 and the Fuel cell regulator for $750. They must be installed in this order though as the fuel cell regulator would be useless if the Highwayman is not running, so the initial cost is $2000.
For some reason, the car won't activate if Smitty installs the car part.