Yes an auto ECU will run a manual car. A manual ECU will not run an auto car. In answer to the differences between the S1 & S2 ECU's, has anyone thought of the fact that S1 run an ignitor on the engine itself, whereas the S2 have the ignitor built into the ECU. Surely that should be a main difference. But if people have responded and said that S1 and S2 are interchangable, then it must work. Realistcally, you are better off saving the money buying another standard ECU and buy a second hand Power FC. They have come down to about $1100.