I do not have too much of exposure to car electronics, but the one time I did work on a car was with the central locking. Rev the engine and all hell broke lose. The fix was to plant a simple half wave diode rectifier followed by a smoothing cap to supply my board followed by the normal regulator stuff. Along with this, there were some kind of coils fitted on the spark plugs that reduced the noise immensely.
Maybe I was plain lucky that my board worked after those changes or maybe it can lead you onto something.
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