Magnum Fuel Inj Without the Beer Barrel

SCT hand held tuner just allows you to simply load a calibration file into the factory ECM. That calibration is setup by the vender that sells you the hand held tuner box.
You supply them all the details of your engine, trans, vehicle weight, etc, and they build a file to optimize the fuel and timing, and shift points if applicable.
You cannot make these adjustments on your own with the SCT hand held tuner box.

Exactly as described above, plus a good tuner will have you report on your wideband readings at idle, cruise and full throttle several times while he dials in your fuel and spark maps to optimize them.

I have run the same factory ECM with several iterations of a 5.9 Magnum from mildly modified stock motors with headers, cam & valve springs and modified Beer Barrel to an aftermarket ported aluminum Eddie headed 408" stroker motor with a pretty big custom cam and 45lbs injectors. My latest iteration spins out 382 hp & 525 ft lbs of torque at the rear wheels, gets 17 mpg at 70 mph and 14 mpg around town.

I get a base tune from my tuner on the east coast, download the file into my SCT Tuner and plug the tuner into the OBD2 port in the car. I drive the car, report back on the wideband readings and upload the corrected tune. It usually takes about 3 fine tunings to get it right.

Chris at Performance Injection Equipment has been the best tuner I have used out of 3. Here's his website.

Mopar Crate Engines, Cylinder Heads & Fuel Injection