I've got a 99 scrambler and the clutch rubs the top of the cover, what might it possibly be? Could it be out of alignment? Also do you need any special tools to be able to remove the starter for a rebuild?

 

You may have stepped on it, or bumped it down. My Trailblazer does that from time to time and I pull up from the bottom of the cover while its running until it goes away. One of my kids used the cover to climb on the bike! No this is not the best fix but it works for me.
PD