How is the O2 wired differently? It is just 3 wires. The ground, 12V for the heater, and the low voltage signal wire. Are you saying that the O2's in an automatic have a different pin out on their harness. I seriously doubt that. What exactly is different? Is the signal wire going to a different pin on the computer so the harness you are talking about is the one between the connector on the O2 and the plug on the ECM?
Very strange. Why would they do that?
Let me try to give you an explanation:
Its not that the O2 sensors - or their function - is any different between MT and AT cars, its that the O2 sensor
harness is different.
The EEC uses many sensor inputs to determine strategies for engine operation under various conditions. One input the EEC uses to determine idle, and idle down (ie 'dashpot'), strategy is transmission gear. The EEC is 'signaled' by 'grounding' pin 30 so it 'knows' whether the transmission is in gear or not. For MT it uses the NGS (mounted on the top cover of the T-5) and CES (mounted on the clutch pedal) which connects pin 30 to pin 46 (SIG RTN, an EEC internal 'ground'). For AT the NSS is used to signal that it is P or N by using the same circuit that is used to connect the starter solenoid to the ignition switch. When the AT is in P or N pin 30 is grounded thru the internal 'coil' of the starter solenoid.
Ford essentially used two sets of circuits (wires) to deliver the MT or AT signals from the respective transmissions to the EEC processor. Presumably for cost/commonality reasons
both sets of circuits are contained within the main EEC harness. The determination of which circuit is used is made via a specific 'jumper' wire. The jumper is different for MT and AT. Ford put the jumper in the O2 sensor harness, therefore there are 'MT O2 harnesses' and 'AT O2 harnesses'. From arms length (and even closer) the MT and AT O2 harnesses appear identical but under close examination of the 8-pin connector where the O2 harness connects to the main EEC harness you would see a difference in the pinout position of the jumper wire. So although we all call this harness the 'O2 sensor harness' it actually contains more functionality than that. Just for the record the 'O2 sensor harness' also contains the wire for the 'low oil' sensor which is mounted on the oil pan and also has nothing to do with the O2 sensor function.
The A9L vs A9P processor issue has to do with the fact that on AT applications the pin 30 ground signal in P or N uses the same wire that is used to supply battery voltage thru the ignition switch to the starter solenoid during START. So during START pin 30 will see battery voltage because the AT transmission 'signaling' circuit is wired that way. But its only wired that way when the AT specific O2 sensor harness is used. I cannot verify that certain processers are 'immune/vulnerable' to having battery voltage on pin 30. I have read that the AT processors (ie A9P, etc) are 'immune' and that MT processors are 'vulnerable' (A9L, etc) to being 'fried' when battery voltage is put to pin 30. That is why it is said that it is OK to use an AT processor in a MT - because in an MT car (with an MT O2 sensor harness) pin 30 does not recieve battery voltage in START, but not visa versa. More importantly though is that when the 'wrong' O2 sensor harness is used (ie an MT harness on an AT car) the EEC will not recieve any signal at pin 30 because the correct jumper for the necessary AT circuit will not be there. And that can/will cause issues with idle and idle down (ie rough idle, stalling, etc). That is why I feel it is incorrect when it is said that all you need to do is use matching processors and O2 sensor harnesses - regardless of the actual trans in the car. For example if you have a car that has an MT and you use the EEC processor and O2 harness from a donor car that was AT although the processor and O2 sensor harness 'match' the processor will not receive the transmission signal at pin 30 because the jumper in the AT O2 harness is incorrect. The best way is always to match the transmission, O2 sensor harness, and EEC processor.
I hope this explanantion was helpfull.