welcome dirtridernh!
I'd replace every bearing and every seal.
Completely go through the tranny, and replace any gears or parts that look questionable, usually 2nd, 3rd, and 4th gears will show the most wear. Check to be sure the forks are within spec and not bent. Be sure to replace all the snap rings in the tranny!...or it could come back to bite you later, then you'll have to split the cases again to replace a $2 part. Check the shift drum for excessive wear...and check the shafts real good too.
What connecting rod do you have?...hopefully an OEM or Wossner.
Check your cylinder's intake bridges and exhaust ports real good for cracks.
I'm sure other members can come up with more things to look for, but this will get you started.
here's a good link to read...it's LONG, but if you read it carefully, there's a LOT of hints and tips...
http://www.kxriders.com/forums/index.php/topic,8717.0.html here's a couple good ones too look through...
http://www.kxriders.com/forums/index.php/topic,12120.0.htmlhttp://www.kxriders.com/forums/index.php/topic,11657.0.html