On my '82 650 the clutch has always knocked like that. It gets worse when it's cold and/or in neutral. When it's in gear it almost goes away.
It sounds like what you're talking about is the clutch rattle you've read about. I've found adjusting the clutch adjuster screw on the cover helps, as well as adjusting the clutch cable.
Also, if you sync your carbs it will help immensely. Something about the pistons fighting eachother when it's out of sync really enhances the clutch rattle.