I checked the valve gaps and they are all perfect. I did find a kink in the air check valve tube and rerouted the hose. I attempted to sync my carbs but #3 barely registers, as does #1. #2 and #4 were matching each other and at very good levels until I unkinked the air check valve hose, and now all four are barely registering any movement on the needles. But they are in sync

I checked my timing belts because I have had a few monster backfires and the right timing gear was off about two teeth, maybe a bit less. Corrected that and cranked the bike for a few seconds (no coolant in the radiator yet - cleaning it tomorrow) and wow the nasty clanking, sounds like it is from the left side of the engine.
I did the finger-compression test and #1 does feel weaker but not by a lot. #4 seems to have some oil seepage at the top of the threads, and all of the plugs are dark and slightly fouled. Sooty, and sooty pipes. I'm 2 1/2 or 3 turns out on each of the four lean/rich screw valves, and am stumped.
I really want this engine to perform as perfectly as I can get it, and I do not want to blow it up. I will order the air check valve kit tonight or tomorrow, but would love some ideas I can work on while I await delivery. [edit] - RPM's above 1500 eliminate the hard knock, and I have tested it up to 4500 RPM with no problems. It is not chain slap, I do not think. I am used to that. This is more sinister.