Back in the early 2000's when we would swap a manual transmission into an automatic Ford Focus you would have to reflash the engine's ECU to forget about the automatic PCM. It was a pretty common thing as the ECU's were supported by the aftermarket (Diablo Sport, SCT, etc..). Given the aftermarket hasn't really embraced the TC I would doubt this is going to be an easy task.
Does anyone here know if the Focus ECU and the TC ECU are the same?