Engine swap questions

PCM does control Automatics, and will throw codes if all of the sensors from transmission and rear end are missing. Just putting a PCM for a manual transmission will not keep all the codes away. You would need to send it in to someone to get a custom flash to turn off what you do not need. You can get recommendations from dakota-durango.com on who is the best. I would get the PCM and engine from the same vehicle. Some of the different years computers will not communicate with another years sensors.

Example.. I had a 98 318 5 speed Dakota and swapped a rear end from a 99 Dakota R/T into it. Speed Sensor had to be replaced for the speedo to work.