I would assume there would be converter lock up and OD solenoids an auto trans computer would want to see, or you might like to have that wouldn't be present in a manual trans truck computer. Might also be a park/neutral switch that may not be present (1st gen Dakota didn't have a clutch switch and would crank with the turn of the ignition switch without the clutch depressed) that would be a nice addition for the auto trans. Transmission kick down linkage or cable wouldn't be present in a manual trans truck either.