According to the Urban Dictionary here is how you "Clean your Clock".
1. Clean Your Clock
A slang phrase meaning to strike a blow to the face, where someone's face is their 'clock'.
Steve: Wow john, you blew it there.
John: Oh shut up, or I'll clean your clock.
2. clean your clock
means to thoroughly take someone to task
Brian was spreading false information behind Mark's back, Jared told Mark about Brian then went back to Brian and said " Mark is going to clean your clock!"
Or...if you take it to mean to help someone than this one would be the meaning.
1. Wouldn't getting your clock cleaned make it run smoother? Is that the original meaning? To take one to task so their mental facilities start clicking?
So which one works, cause we know that the clock doesn't.