So my 02 f4i has a cam chain noise when riding over 55 mph or when heated to about 160 degrees. It sounds like the chain is rubbing the case but it only does it when the clutch is out . If I pull the clutch in the noise goes away. I just installed a manually cct that was installed correctly What is causing this?

 

Sounds like you are describing a bearing noise not a clutch issue. Take it apart and inspect it piece by piece as you go. You might just find a toasty bearing behind the clutch as long as the button that actuates it isn't all ground off.

 

I can hear the noise coming from the top of the motor and down at the bottom and when I recently changed my clutch it looked like there was rubbing marks on the case from the cam chain.

 

Try re-adjusting the cct. then let us know. If the noise is coming from top and bottom of the engine both it's either valvetrain related or the noise you are hearing is traveling. Use a solid rod, like a long ratchet extension to press against the engine at the top and then the bottom (as a stethescope) this will clue you in as to more precisely where the noise is coming from. They do make cheap stethescopes for automotive use as well (sears carries at most larger stores in the automotive tools section).