2006 yz450f making noise

So long story short bike got hit on trails skipped timing get it home take it apart replace parts start it and now it's making a nasty tick noise or knock. Noise is a lot stronger on the clutch side and doesn't increase with rpm! Any help would be greatly appreciated!!

Clutch looks fine. So how much play should be in the water pump? And does the water pump speed up with rpm?

The water pump is engine driven, so...

 

The pump impeller can normally be rotated about 20 degrees or so back and forth.

 

If you have an aftermarket skid plate , remove it to see what it sounds like then.  Does the noise stop when you pull the clutch in?  

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