You are correct, they do sit higher.
You can use the original seat tracks and this will lower your seat height, how ever you will need spacers and two longer bolts for the front of the seats as the 99-04 driver's seat has a dip or low spot in the front and the 94-98 seat is flat. You will also lose the function of tilting the bottom of the seat by using the 94-98 seat bracket, but the height adjustment for the bottom will still work.