Be advised here. The programming of the PCM is different between the manual and automatic transmissions. A replacement PCM will need to be sourced or, your existing PCM will need to be reflashed to reflect the transmission change.
It is not a simple "bypass the NSS" situation. There are significant changes in the PCM. Ignition timing being just least of them. Plus, the PCM will be looking for the TCM and will. most likely, fault into "limp home" mode if it can not find it.
For any given model year, Jeep had 6 versions of the PCM.
AUTOMATIC TRANSMISSION
49 State Emission
Low Emission (California)
Export emission
MANUAL TRANSMISSION
49 State Emission
Low Emission (California)
Export emission
When you source the replacement PCM, the VIN will need to be flashed into the replacement. Keeps both the Feds and your local Emission Inspectors happy...