That.... could be problematic, should a police officer or state inspector compare the VIN plate to the stamped number. The stamped number is the one they consider "official".
If you go to the search page and run a search for "title" you'll find numerous threads where people have to get new titles for their bikes.
As to the bottom-end noise, these bikes can produce a fair amount of chatter at idle, it's often the cam chain (adjustable) or the primary chains (not adjustable). Does the noise change when you pull in the clutch lever at idle?
mystic_1