Hi there, I'm just finishing the 5mt swap into my 97 legacy. The pin you need to ground is #81, but on the auto cars, there is no wire there, just an empty slot in the plug. I had to remove a wire from pin 79 (79, 80 & 47 are used to talk to theTCU which you don't need anymore) and plug it into slot 81. I then soldered that to a power supply ground on the same harness, but I forget which pin that was right at the moment. This will groung that 81 and the ECU will now think it is a 5mt ECU. After scanning for trouble codes, the code it was throwing was now gone, no check engine light!!!
Rallitek rocks by the way! Sean totally hooked me up with the turbo setup I'm running right now and tuned it with the Perfect Power 6. It runs awesome! Good luck with the rest of your swap, and PM me if you haave any other questions.