The factory trans is controled by the factory ECU/ECT so when the V6 is removed the trans will not have any electronic control and will not change gear. When running Auto box I generally use the lexus Auto with factory ECU/ECT unit with the 4x4 transfer box on the back. Another way is a separate aftermarket trans control ECU which I believe spitronics do one and so does the Wolf V500 ECU(wolf is engine trans combined). Cheers