My first thought on putting a 2000 or later ECU in a 1999 or earlier is that the ECU connections are very different.
2001:
1999:
Can it be re-wired? I'm sure it can, but it's not going to be a simple matter of looking at pics from Googles.
Next, Cable throttle vs Electronic throttle. -Adapt the throttle, or adapt the gas pedal.
That's the easy stuff for me to point out. I'm pretty sure that the '03 and '04 ECUs are going to be looking for some CAN Bus input, but I haven't looked at specifics. If you have a full car to pull parts from, it's probably not that bad.