A couple of questions for you that might help in understanding.
Does the sound change with engine speed?
Is it different when it's cold or hot?
Does it change if it's in gear or neutral, clutch applied or not?
Does it change when you put a load on the motor (i.e. start moving) vs. Neutral and not moving? Or does it remain the same no matter what?
I'm sure there are many fine questions that I havent though of.
Wrong side of the bike, but did you check the counter balance shaft adjustment?
It will make a racket if its adjusted improperly. There's probably other thing to consider but sound travels in strange ways in a crankcase.