The A9L 5 speed computer has more help in the Tweecer department. The Tweecer is a portable programming tuner that attaches the Mustang's computer to a PC or laptop loaded with special tuning software.
The A9P is the auto trans computer which will work with either the 5 speed manual or AOD automatic trans. The inner workings are almost identical, except for the EPROM. The A9P supposedly has a different timing advance curve programmed in the EPROM..
If I understand it correctly, the thing to look out for when swapping one for the other is neutral saftey circuit at pin 30 of the connector. The A9L (man trans) uses a lower voltage signal then the A9P (auto trans) which I've heard uses a 12v signal. So if a A9L is used with an automatic trans harness, it would fry the computer. I've also heard some people just snip that wire, but then the computer does'nt recognize when the car is in gear and could stall because it does'nt recognize the extra load. I've also heard issues with not being able to pull codes with out that circuit. Double check this info before you do anything, I'm just passing on what I've read in other forums and don't have any firsthand experience with this.