cracked heads, head gaskets. Pressure test the system, does the exhaust smell like anti freeze? You should of done that first. Diagnostics is always better and cheaper then just throwing parts at it hoping you fix it.
Did you do a complete chemical/pressure flush of the block? I did that when I replaced the complete system on my '03 4.7, and it's run cool as a cuke ever since.
I have a 2002 3.9 as well, and, if anything, mine doesn't run hot enough. The temp gauge gets to the 1/4 mark and stays there.
What I would do in your situation is drain enough coolant so that I can barely see fluid in the upper rad hose with the cap off (ensuring the cap is at the highest point in your cooling system), then use an infrared thermometer to measure the temperature at the thermostat as the engine warms up. At the thermostat's set temperature, it should start to open up and you should see coolant pumped from the engine towards the radiator. Flow should increase as the thermostat fully opens. Shut off the engine and put on the cap when the coolant level rises to threaten to overflow. This process should tell you if your water pump and thermostat are working right.
When I did mine -- it was because I was in there and everything already had 150K on it. And I knew the radiator was clogged so it follows that the engine cooling jacket was likely also getting clogged up. It was little extra money, maybe $200 more to do it all. The question is really why WOULDN'T you replace everything? Once the radiator is out, you have easy access to every part. No time like right then to put in the new pump, idler, serp, hoses, stat, fan clutch, and install a flush tee. The only thing I didn't replace were the heater hoses -- those are easy access anytime, and mine had been replaced at least once already.
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