I don't believe that's true when it comes to the fuel injection. 99 and 00 are essentially the same. My PC3 works for those years only, and modifies the signal from the ECU to the injectors. The PC2 actually modified the signal from the sensors, to which the ECU then sent the appropriate signal to the injectors. Since the 2001 and later has an O2 sensor (i.e. feedback), Dynojet had to go back to modifying the input sensor signals, which is why it plugs into the ECU, like the old PC2.
However, if you have a way to (electronically) delete the O2 sensor from the ECU, I don't see why my PC3 wouldn't work for the later years.