Ok just checked Toyota manual, it is the same box. ECT equiped tranny got a different ECU with bigger plugs.
This acturally make it worse. Someone gotta specialize a chip for that ECU. Its already hard to get ECU chip not to mention ECT E CU

On another note, the ECT measure engine torque and adjust shift point accordingly. So you may not need to change anything. Maybe just change the torque converter?
You could probably connect switch directly to the solenoids and bypass the ECU for manual shifting. Don't know if that gonna grind the gears or not.