Slightly bent timing shaft does it.
If I can find the post (archived by now), I showed how to straighten this up with a dial indicator and a few judicious taps of a small hammer.
Description:
You must remove the timing plate and spark advancer, leaving you with a long, thin shaft that sticks out of the end of the crankshaft. Mount a dial indicator to the engine block and measure the out-of-round run of the shaft, about 1/4" down from the threads. Tap with a small hammer to recenter-ize it (is that a word?). You should be able to get it within .002" with patience, and this patience pays off later. I think Honda's spec is a generous .010", but I've seen this still leave jitters behind.
This shaft has become non-concentric over the years, probably from someone yanking left-right-left-right on the big crank nut while setting the timing with a light bulb, which was (is) a popular method. The spark advancer has just one locating dowel in the end of the crank, so it loads this shaft sideways when you do that, then bends it a little. I never remember these being bent until the owners read these articles in Cycle World magazine in the early 1970s, and then they would bring the bikes into our shop, obsessing about the timing jitter (which generally adds a hint of vibration at highway speeds, but no other problems. Back then, I used a bent coat hanger, clamped to the frame and pointing to the end of this shaft, to align it: I was too broke (in school then) to afford a dial indicator, like the Honda bulletin said...

So, I just got it as perfect as I could, and it usually worked out fine.
