Look at the back of the bike and see if the rear fender is straight with the rest of the bike. If not the sub frame is bent. I just replaced my bent aluminum sub frame off my 05 ec200 with a 94-98 KX sub frame. My rear fender was shifted by 2" and the rear tire was actually hitting the muffler. When I unbolted the seat the seat base was broke into several pieces.
http://www.gasgasrider.org/forum/showthread.php?t=21311
Also check your forks to see if the fork guards are wearing through the upper fork tubes.
http://www.gasgasrider.org/forum/showthread.php?t=21312