There is a hardware difference between an auto processor & a manual processor. The difference is because of the way the NDS [neutral drive switch, manual transmission] & the NSS [neutral safety switch, auto transmission] are wired. They are both wired to the same pin#30 but the auto trans wiring grounds the pin to the starter solenoid & the manual grounds to signal return, during crank mode there is a voltage spike sent to pin-30 so the auto trans processor has a diode on pin 30 where as the manual processor doesn't, most of the time this won't cause a problem unless you get into a prolonged crank condition.
Those that want to convert their automatics to manuals, and swap the ECM, need to clip the wire going to pin 30 or else the ECM will fry the trace off the board. This leaves the manual EEC unable to dump codes, which looks for the loop through the neutral sensing switch of the T5 transmission.
Make sure you have a 5 speed O2 sensor harness when using an A9L or you will fry the trace also. The damage is common when people mismatch harnesses and use an automatic O2 sensor harness with an A9L computer.