After all this talk about ferrite chokes, I still think the best thing for you is to separate signal wires from power wires, and to use drain shields on the most sensitive wires (ignition trigger, injector PWM). I have only used chokes in automotive to filter audio power from the alternator. All things EFI are separated and sensitive signals get drain shields. Most of the time, only injectors, ign triggers (hall or VR from dist/crank and back from ECU to coil), and O2 sensors. Chokes are great for filtering line noise from motors and things, but aren't exactly a go-to for automotive.