How many miles cam? A common noise is caused by a loose timing chain, especially when decelerating. Mine did this after i adjusted the valves . Putting the bike in 5th gear and rocking it back and forth can sometimes make the adjuster take up another notch and cure it. Some of the earlier chain guides failed, but my 07 had the newer style.
I know the drain plugs moved at some point, but i don't know why. Mine are not as shown in the manual, but I've never lost any sleep over it.
Its a big sloppy engine with a big sloppy transmission. It does tend to be noisier than other cycles. I call it personality.