It's been a seriously long time since I used OS9, so I'm a bit sketchy on some of the details now.
Probably, the first thing you want to do is disable some of the later additions to your extensions. From memory, the interaction between certain extensions can cause some major fails.
First try booting with the shift key down. This enable a safe mode. You should see which extensions are loading and in which order.
If everything works okay, then it's a matter of finding the culprit extension.
Failing that, try disk first aid. It may help. Or Nortons Disk Doctor, or any other disk utility you may own (I forget what others were available). Nortons was a quality product back then, so should fix most issues.