A9l is a 5 speed computer,I have the same delema. heres a thread on it.
http://sbftech.com/index.php/topic,25116.15.html
This issue is only applicable when swapping EECs withing the confines of the original factory wiring harness. The way these came from the factory the jumper wire to input into pin#30 of the EEC was contained in the HEGO harness, so you had two different part numbers for the auto vs. manual HEGO harness.
Once Ford started selling the harnesses as retrofit pieces, it was available under different part numbers. M-12071-C302 is the main harness.
M-12071-E302 is the engine/injector harness, this also contained two different HEGO harnesses, one for the auto and one for the manual. The harness/EEC really does not care one little bit about what tranny is in the vehicle, it's just so the correct input is plugged in for pin#30. This harness was based on the '93 Mustang wiring.
Once Ford started selling the new EFI project harness, 12071-A50 it uses a totally different design which incorporates a RCM that uses a logic circuit to prevent the EEC from setting the code#67 and allows the Cylinder balance test to be conducted without actually simulating "neutral".
In this case the guy is already using an A9L, so it makes no difference what tranny he puts behind the engine, as long as it's already working, nothing will change.
My $.02
Joe