What you describe sounds exactly like what I ultimately found was a loose fitting gib key. I can't hear it in your video, but the sound in mine sounded like it was coming from the crankcase. I found on my PowerSolutions 6/1 that the gib keys were narrower than the slot milled in both the crankshaft and the flywheel. Total clearance was about 0.019" if I recall correctly. No matter how tight I pounded the gib keys in, on power strokes, there was enough torque to twist the crankshaft against the flywheel, and when it came up tight, it made a "clunk" sound that went away immediately when the decompressor lever was engaged. Do yourself a favor and before you go tearing the big end off the rod, pull a gib key and measure the width, then measure the corresponding width of the slot in the crankshaft. They should be within a thousandth or so.
I fixed the clearance by taking some pieces of 0.005 and 0.010" brass shim stock, cut with scissors to slide between the side of the gib key and the crankshaft groove, and also the flywheel groove. Once I tapped the gib keys in, the noise went away.
Now, it's also possible some of the noise is from backlash in the idler to cam drive gear. That one is more difficult to fix and involves machining an offset idler pin to allow you to adjust the mesh of the idler gear. Once you get these engines dialed in, they run fine. But the way they come from India, all bets are off. Every engine is an individual.
Quinn
P.S. Here's the link to the thread from 2009 when I described what I did:
http://listerengine.com/smf/index.php?topic=962.msg12839#msg12839