Yup, that lower rod bearing is a goner.
Time for a lesson in splitting cases
-- Ray

I see the wrist pin moving, I'd say your pin bearings need to be replaced or perhaps someone put the wrong wrist pin in?  Not an expert here, just guessing

Uh oh….. Every one of my bikes sound like that video 

IMHO, video in post #9 appears meaningless to me. Seems to be bone dry with no oil. New parts almost certainly will click like that if dry... especially the piston movement.

(clean all the oil from a new crankshaft ball bearing and shake it... it will rattle... doesn't mean the brand new bearing is worn out!)

Silly idea... why not actually measure the big end bearing wear as described in the service manual?

If you hold the piston at mid stroke, then rotate the flywheel back and forth you will quickly see/ feel any play in either the big or little end. Now that the cylinder is off, you might want to put two equal blocks across the crankcase under the piston and let it find its natural alignment with the con rod. Hold the piston stationary and rock the flywheel. Any play at all and the bearing needs to be replaced IMEDIATELY. This is especially true of the big end, because it's replacement is often avoided if possible, but failure is catostrophic.