As with many survival related expedient repairs some of these fixes could present a fire or mechanical danger. As always work/learn with a responsible experienced mechanic, one who specializes in off road racing will often have good experience in how to squeeze a few more miles out of a damaged vehicle.
Diesel Engine Glow Plugs: if the glow plug control system goes down try running a parallel power wire from the plugs straight into the cab off of the fuse panel or cigarette lighter, try to determine amperage draw ahead of time for proper switches and wiring. Power the plugs for 5-10 seconds before starting, shut off power to the plugs once the engine is running. Fuel pump: if you have an older manual carbureted model you can drip feed a carburetor, better still a gravity feed into the fuel intake will let the carb work normally.
Fuel Injection: A real problem; in case of failure a replacement intake manifold or adapter and aftermarket carburetor is the best bet, keep a set in the shop for emergency. Write in with suggestions for a diesel with electronic fuel injection (EFI). Vacuum line hose and plugs: even the spark advance
and brakes can be plugged but engine performance and braking power will suffer, most lines run to clean air gadgets.
Air Cleaner: try using pantyhose or open cell foam, be creative but be sure that it is not going to get sucked into the intake potentially ruining the engine, window screen over the throat of the carb is advisable if attempting a homemade cleaner.
Smaller engines can often be modified for crank starting, but beware kickback, look at designs for crank-started cold cars and farm equipment.
As for motorcycles an off road bike with magnetos is a good choice, how I miss my ’93 Honda X-200R bugout special. Seek one with electronic ignition over points (the EMP required to destroy this high energy rated circuit would require a detonation so close by that the bike would be destroyed by heat and blast.) An electronic ignition lasts much longer than points with no maintenance required until failure.
Here is a site with some useful information on magnetos: http://science.howstuffworks.com/question375.htm
Someone who has access to a shop could modify a diesel generator motor mount to fit a motorcycle frame, a 12 VDC motor (scavenge from a car junk yard) could be built into a hand crank generator to light the glow plug if a bike without battery is desired. A cable clutch or centrifugal clutch is needed, possibly some motorcycle transmissions will mate with a diesel motor, e-mail in if you know of such a motor/tranny combo.
If your vehicle is designed for survival applications don’t let EMP fears be foremost, instead pick an easily repairable long lasting design that conserves fuel and other expendables. For the most part even EMP aside maintainability still leads to an electronics sparse vehicle. In truth as long as there is power for the ignition everything else is optional.
If EMP is truly a fear you can’t put out of your head, [removing and] wrapping in aluminum foil of the more sensitive electronics containing ICs (integrated circuits a.k.a. computer chips) will put you at ease. As I have written before, EMP is not a realistic concern for most vehicles, look at older EMP posts. Don’t swallow the Hollywood/TV science that EMP attacks will completely destroy vehicle electronics. EMP is most likely to damage electrical and communications infrastructure, while leaving most vehicles functional.