I am trying to replace a 1998 ford explorer 4.0 engine with a 2000 ford explorer engine 4.0. what type of customizing of parts will i have to do/

Your 98 4.0 is the older pushrod type engine which, in my opinion is a much stronger engine as it is within an engine type manufactured for previous decades. The 2000 V6 4.0 is a single over head cam engine. It produces about 25 more horsepower than the 98 version. I have four explorers containing both engines. The pushrod engine with 25 less horsepower is not noticeable less powerful. If you are swapping out engines I recomment both the front and rear cam pulley guides be replaced before the engine is installed. These are ware components and when they go you get a slapping noise, sometimes perceived as a knock. Either one is difficult to replace. The front can be replaced with the engine in the vehicle. The one is the rear, which runs the other bank of cylinders requires the engine be removed from the vehicle to service. You may have to bring along the EVAP system for the older engine, but not sure. The PCM may also have to be updated.