Any electronic/electrical device will fry if not shielded or hardened, so you will need to store a alternator, battery sensors and a ECU in a shielded container. The container does not have to be lead lined, there are other shielding schemes that will work just as well. It would be eaiser to store a complete engine with sensors, ecu etc together. Most fuel pumps should survive in a full tank of fuel.
Get a early 8valve and go with a myside2 and store extra ignition/battery/sensors.
Swap in a mechanically injected diesel.
If a EMP blast hits dont forget the gas stations can no longer provide fuel in the conventional manner, make sure you have equipment to retrieve fuel from the underground storage.