Using logic, if the noise stops when the clutch is disengaged the cause is downstream of the clutch, so no camchain or crankshaft problem. Determining the etiology of the noise is going to take some doing, but is limited to the transmission / oil pump / water pump which at least narrows the focus.
Sound is a good way to narrow the focus further. At idle the crankshaft is turning ~1200 RPM, or 200 RPS (Second). This rotates the clutch at ~800 RPM, or 13.333... RPS (1.52:1 reduction). Counting the cyclic noise in the video against the counter yields a period of 0.5 second. Given that information the task now is to find a transmission component that makes a full revolution at that RPS. Here is a good source of information that can shed some light on the problem : 
It has listings for thousands of motorcycles' drive lines. And there it was: the second gear on the countershaft is twenty six teeth, resulting in a period of 0.5 second. It's located next to the output bearing, which means that when the chain wrapped around the front sprocket the forces flexed the bearing, countershaft, and the engine case enough to damage the teeth then in contact with the matching mainshaft gear, damaging at least two teeth.
I may be off base here, but logic indicates it is a strong possibility. Frankly, I hope I am wrong due to the fact that the engine will have to be partially torn down to effect repair.