You have to understand just boxing computers and other microchip boards in a vehicle won't really work. The farady cage is going to stop the impulse from directly impacting the microchips, but any wiring into the board is going to act like an antenna and channel the emp from outside the cage to the board and fry stuff. Essentially, unless all wires entering and exiting a cage are set up to stop the influx of energy, the cage is putting a bandaid on a sucking chest wound.

If you garage your vehicle, the best thing to do is turn the garage into your controlling system. Cage the garage. Only problem with this is figuring out how to ground the cage. The ground has to be corrctly done or it will fail. Some of the tests on this concept that I've read point some amount of protection even if done without grounding.