As standard the ap engineering ecu only accepts an on/off tps signal.
Without knowing the exact pinout of the ecu I wouldn't know whether there is the provision for a variable tps input, but I would say it's a no I'm afraid.
As for the map sensor, it shouldt be any different between manual an auto, but you can fit any 0-5v map sensor and just input the scaling values to get it to work
That would be the best idea. I'm not sure if the auto tps has an open and closed position feedback with the 4th pin being the variable feedback? If so, it may be ok to keep it, as long as the pin o/p goes to the right pin on the ecu.