I think the only real consideration would be the fuel pump. The EFI pump is buried in the gas tank and I would think it would be a higher pressure than a pump for a carbed engine. You would have to rig some sort of fuel pressure regulating system or swap out the assemby in the gas tank. Ultimately, the EFI pump would be better than the carb version pump since the EFI is in the tank and the carb version runs off the cam on the engine(??). Since pumps push better than they suck you'd get better performance.
Ultimately, if you can come up with one, go with the EFI motor. I've had my EFI '85 4Runner for 11yrs now and would never have a carb in a 4x4 again. EFI doesn't care what angle you are sitting at or how big the last rock you hit was