The carbs also make a ticking noise as well which also can be a normal sound.
There is also a possibility that you have a slight slide rattle, which can be heard more at idle and tends to go away when throttle is applied. Even though we have Keihin carbs this info about slide rattle from Mikuni may help a little since they work similar.
http://www.mikuni.com/c-faq.html
Also some info from Factory Pro.
http://www.factorypro.com/tech/needle_jet_wear.html
To me, it sounds like your rattle may be somewhere in or near the exhaust, but also some from the engine. You may have to really try to pinpoint where it is the loudest. (exhaust or upper cylinder head)