The change in part number from year to year could be something as simple as the seat cover color/material/stenciling - makes it really hard to cross reference for physical fitment.
Someone familiar with the older bikes ("D" models or early "E" models) might be able to answer your question, but I would suspect that the E1 and up models all use the same seat base.
Here's a link for reference -
http://www.kxriders.com/forums/index.php?topic=2962.0Another way to assume fitment is search out replacement seat foam, which I believe fit 88-04 kx500's... another suspicion is that the seat base of a KDX200 may also fit using KX500 foam/seat cover, but this is truly just a guess.
Hopefully someone can give you a definitive answer and good luck in your search!