interface with automotive pwm fan contoller

if you are using a mega, i can do you one better:
http://arduino.cc/playground/Code/PwmFrequency

the spec sheet says it can take PWM or LIN, lin is a simple bus comm protocol, sounds like it may uses the 12 v line to work its magick, and I would hazard a guess you have a snowballs chance in a hot place to figure that out. stick to the PWM