Yes I tried this and it seemed to work as I went through all the stages successfully. However, when I tried to start the car, no crank. I now realize this is due to the fact that I used the new key transponder (as commented by Abel).

But if the synch actually worked, why is it that when I put back the old ecu and started the car with the old key transponder, it started right up (but still with the misfire that I am trying to cure with an ecu swap)? If the synch worked, then a new ISN should have been written to the EWS right?