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I'm sure others who know more about the PFC will chime in but here are a few answers to your questions -
With the Commander you have to start with the default map. You can't load a custom map. But you can change parameters such as injector sizes, sequential - non-sequential, some stuff like that. You can also vary the amount of fuel in each of the 400 cells (although it is a little tedious with just the Commander). Same with both ignition maps. There are ways to richen just portions of the map with PIM voltages, fuel increases by RPM band, etc. You can also richen or lean out the entire map at one time by altering injector lag times.
I'll let others suggest what you should or shouldn't do without getting a professional tune. On my own car I did start it and let it idle on the base map. Just make sure you warm it up before you shut it off or you risk flooding it (ask me how I know). All engines are different but mine didn't drive well on the base map until I got a Datalogit and started tuning for AFRs.
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