Better late than never.
It always bothers me when someone posts a problem on a forum, accepts a ton of advice and then disappears, never to be heard from again.
So this is my final post on the outcome of the "Knock, knock" .
Over the winter I removed the engine, tore it down and measured all crank and big end bearing clearances. All the bearings measured within spec.
Only the #2 big end bearing measured at .002" clearance, the upper end of the spec. Since everything else looked fine I was determined to change something before I put it all back together and #2 bearing was the only thing that wasn't perfect. The good folks at Silver's Spares found the size I needed in Belgium and shipped it to me. With the new bearing installed I "closed up the motor and re-installed it" (7 words, 3 months).
I set all the pilot screws at 2 turns out and synced the carbs. Also tossed all the emissions stuff and the vacuum fuel valve.
I started it up in May and let it warm up (remember the knock only appeared on a fully warmed up engine). No knock. A few weeks later I rode it about 30 kms, no knock.
So i guess I'm still not really sure what caused the knock, bearing or carb problem. But it's quiet now, smooth and powerful, I love this bike.
Thanks to all of you who offered advice. Special thanks to Uncle Phil, and the BIG GUY, Allen Millyard.
Ride safe!
Paul