Is the automatic transmission controlled from the ECU, or is there a separate transmission control unit?

The engine control unit (ECU) only does the engine - there is a separate transmission control unit (TCU) that operates the automatic transmission.  The ECU and TCU do not talk to each other. The TCU gets information regarding throttle position, RPM, etc. by sharing the same sensors used by the ECU.

On 2Gs, the TCU may communicate an error code at the ECU, so the "Check Engine" indicator will light, but that seems to be all. Apparantly, the ECU and TCU do not communicate in any other way.