Help with stock EFI

The OBD2 Magnum fuel injection system will operate the engine just fine in stock configuration without the transmission plugged in. The speed density system uses manifold pressure (MAP sensor) and throttle position (TPS sensor) along with how fast the engine speed is increasing based on crank shaft position sensor rate of change, or how quickly it is accelerating. It also uses coolant temp and intake air temp so you need to keep those sensors.

Further, the RE transmissions are not fully electronic anyways. It is a weird electronic governor system that the PCM uses to basically manipulate the governor pressure to cause the transmission to hydraulically shift when conditions are right.

If you have an OBD2 PCM identified easily by three connectors, like the one the OP is getting, and you plan to get it recalibrated anyway, the SCT software has the option to select a 3 speed automatic trans, a manual trans, or the 4 speed automatic. So if programming anyway, don't worry about the transmission the truck originally had. If it had a 3 speed automatic or manual, it just allows you run it without setting transmission codes. That is something the tuner can do when they develop your calibrations to be loaded into the handheld for the end user to load into the vehicle's PCM. The handheld tuner cannot simply select this option.