G'day Musky.
A well made and often overlooked point there concerning the con rods.
As a general observation, big end eyes also need to be checked for ovality. The big end crank journals have a recommended max of 2 thou tolerance for ovality, so you can see any additional problem with the rods will add to this, let alone worn journals or flashed out shells.
As to the source of the knock, anything that moves is a possible culprit. Small end bushes, piston bosses, cracked pistons, broken rings, piston slap, main bearings, big ends.
'54 added to my initial comment, and there is a whole spectrum of noises which enable the well experienced to diagnose by ear with attention to throttle setting, load, over-run etc. Some symptoms are characteristic, but in any event looks like a pull down. Be interesting to see what you find.
The problem fixes are the ones where everything looks normal. Major mechanical mayhem are the easy (if expensive) ones.
Although we are all looking on the black side of things, just make sure there is nothing in the primary side that could be a simple fix.
Cheers.
Swarfy.