One is a return-type system with the pressure regulator on the fuel rail; the other is returnless with the regulator in the tank. The two systems run at very different pressures and require different flowrate injectors. You must match the pump/lines/regulator/ injectors/fuel rails/PCM from a compatible donor or it won't work.
A 98+ 4.0L will be returnless like your 3.0L but this type of swap is still a minefield of potential problems. Staying with the same year donor as your truck is the best way to avoid compatibility issues.
Last edited by rwenzing; 10-12-2009 at 10:54 AM.