Sorry, “parts trucks” sitting around rotting makes no sense to me. I manage a fleet of FMTVs for my fire department and our solution to high mortality, hard to find parts is to stock them on a nice dry organized shelf. Alternator, WTEC controller, keypad, fan solenoid, air brake inversion valve, brake cans, fan clutch, hub spider gears, seals, others. Complete axles never fail. Cat and Allison parts are easily available from the local Cat dealer and Allison dealer.
And to answer your original question, numerous significant changes happened to the FMTVs in 1998, 2002, 2003, 2006, and later. Transmissions, engines, electrical systems.