Video came through just fine and the knock is quite obvious at certain speeds. I agree that knock is more than you should need to accept on an engine that appears to be that well-built.
I wonder if you can slow the video down (slow motion) to get a more accurate idea of exactly where the knock is occurring?
Have you tried simply wiggling the various linkages with your hands under static conditions to see if you can detect excessive movement?
You say tightening the rod makes the knock go away, but also stiffens the engines rotation. However, even making the engine harder to turn, does it still turn over under moderate pressures? If so, perhaps that is what you need to do to get the engine to "wear in" and run quieter, which will probably also slowly free up the motion for the future!?!?
Perhaps the slightest dab of really fine lapping compound on the offending contact surfaces (if they have been truly identified), would be of benefit to the eventual elimination of the knock and the binding?
A beautiful engine like that deserves to run smooth and quite at all speeds, so hopefully you will find the combination of settings that will bring about that desired result!