First, check the easy stuff. Make sure you don't have anything loose that is just knocking against something else. When the bike is cold, or just warm, grab hold of stuff and man-handle it to see if anything is loose and makes the noise you hear. Grab the front brake and try rocking the bike forward and backwards roughly to really compress and release the front forks. Anything? If not:
Two thinks I would worry about. First and easiest (aside from the above) is to open up the primary cover and check the compensator. Make sure the compensator bolt is tight! Also make sure the chain is adjusted.
If not all that, then I am worried about the connecting rods. Get a stethoscope or a long handled screwdriver and start trying to isolate where the sound comes from. If you hear it on both sides of the engine and from the front and bottom (although some will be fainter), that is what I would be worrying about. Find someone with a bunch of experience to help on this to verify the diagnosis before you start stripping off the top end.
Good luck.
TQ