Mopar OEM EFI
I've never done it with the factory ECU but you will need a high pressure fuel pump and plumb the return line somehow into the tank. I've heard of people plumbing the return line into a welded in bung in the filler neck or a vent line.
Using the stock ECU maybe a problem as they have two sensors as it is OBDII, one before the cat and one after. If it doesn't get the proper signals, it could throw codes and refuse to act properly. That's just one factory pitfall. I have no idea what would happen without the factory speed sensors, ABS, different tire sizes, etc. As far as tuning the system I know that some places can get in and change the firmware, but I'm pretty sure you have to send it in for any changes.
Personally, I'd blow off the factory system for a Megasquirt set-up. That's what I plan to do with my truck someday. There's a member here who works for a company that makes a kit utilizing the megasquirt system, I think it's Madscientistmatt and I'm sure he could give you a wealth of information.