Toyota simply spec'd taller coils on the 1999's. And then around this time, there was a big suv roll-over scare. As a result of this, Toyota lowered the 4runner for 2000-2002 for safety reasons (more like because people don't understand that you can't drive a 4runner like a race car).
If you were to see a 1999 side by side with a 2002, theres a pretty big height difference between them.