yea that will work i had to do that when i did a 5 speed swap in my 95. my ecu kept sending a signal to the auto tranny computer and it wouldnt go past 4k unless i was at WOT and that was only every now and then. take out the auto ecu and the regular ecu and put a 5-speed gst ecu. im not sure if the auto harness is independent between the tranny and its computer but check that too, it might give you problems but i doubt it. i hope that helps. good luck