Update - got the alternator cover off and checked the starting clutch gear (large gear), the starting clutch assembly, and all seem nice and tight. Granted, I did not remove the alternator rotor, which would need to come off to physically check torque on the starting clutch assembly as the bolts run home from the engine side into the rotor. Removing rotor appears to require a special "hold" tool to remove primary nut.
Nevertheless, if the starter clutch bolts had become loose, I would imagine there would be some play between rotor and the starting clutch assembly/gear - which there is not, everything is on tight.
At this point, having ruled out the above issue, and I assume the clutch itself would not be the culprit based on the nature of the clunk sound/feel, that leaves the following items:
1. Chain slack/wear
2. Wheel misalignment (corrected)
3. Transmission (shifts fine, at 12K should be insignificant wear, no contaminants in oil, noise/feel remains with no-load)
I will re-assemble, tighten chain slack/travel to 1 inch, verify wheel trueness, test ride, and report back. Thanks again to everyone who has responded and contributed. I hope this exercise is useful to some of you guys!