How would the ref know which ECM it is? The 2000+ ECMs don't have any markings to distinguish auto from manual.
I stand corrected on the year. When we pulled the motor out of the 2000 4Runner it said ECT on it, so its obvious its an AUTO. Must have been a later year when they stopped putting ECT or MT on the ECU labels.
Next question... for someone who has gotten their 3RZ swap passed the CA referee... since my engine came from a 2000 4Runner AUTO, am I required to find a 2000 4Runner MANUAL ECU, or are they not that picky? Can I just any year/model ECU for a coil-pack, manual tranny setup?