What X files are you talking about? If you partitioned your drive - just format the partition. If you installed X over your existing primary OS9 - I suggest booting off CD or ZIP and reinstalling a non-Xed version of OS9. Then just toss X's system and supported files in the trash (option empty to delete locked files).
If you installed X over 9 just delete everything except the MAc OS 9 folder and then use Sherlock to find all the invisible files and delete them through it (They will be deleted instantly so make sure it is an X file ie: not a file that is in the Mac OS 9 folder or a subfolder). Then move all the files from the Mac OS 9 folder to the root level of the HD and delete the Mac OS 9 folder. This works and leaves your OS 9 system in task.
As long as the files is not in the Mac OS 9 subfolder it is an OS X file. Note that some files are not deletable because they are needed for OS 9 to function. When I tried to delete these files when removing OS X for a reinstall of 9 on that partition it generated an error. Just delete files that aren't in the Mac OS 9 folder and you should be fine.