Should go into reservation mode with the wire back to stock as the ALCA module picks up the door data via the CAN network.
One other thing to try is use a relay to give a good signal to the clutch wires. I had a jeep that I did the other day and it was hit and miss as to whether it would do the clutch bypass or not. In the end I put a relay to give it a good ground and Voila it worked everytime. Sometimes the 500ma ground that the starters output just aint enough.