EMP screws up silicon junctions. The only ones in the stock bike are in the rectifier, and with some models the neutral light circuit. So, you'd need a cage/sheild around that. And shield the electrical wiring to it, as well.
If you have electronic ignition, the silicon in that can fry. So, either dump that, or have a points plate spare to slap on after it quits.
Mostly you have to keep the wiring shielded so the pulse can't generate a voltage within the signal or power carrying wires.