It was the gear teeth at the end of the regulator quadrant. As the first picture shows, 4 of them had become distorted and lost metal from the main drive gear grinding on them at the end of the windows travel. The 'clunk' I was hearing would have been the last revolution of the drive gear skipping over these teeth.
Since I'm a stubborn person when it comes to replacing things, I decided to mig-weld-fill the bad teeth and cut new ones. First step was to hammer everything flat on an anvil, then wire wheel off the cadmium plating in the area. I welded the section until it was filled, then ground both sides flat again.
A 3/4" wide half round file proved a perfect fit in the good teeth. I sprayed the area with machinists blue dye, made a cardboard pattern from the good teeth, then scribed the outline for filing. Cutting was done with a thin grinder cut-off disc and the 1/2 round file, finishing with a small needle file to trim the detail. Picture 2 shows the re-worked area.
I have no idea why Mercedes made this piece out of soft, 1/8" thick steel. I'm sure my welds are tougher than this metal was.
Also, I'm not sure why this happened, as I'm careful to not keep my finger on the button when the window is up (wife may have done this, but I doubt it, since the window stays up most of the time for the A/C). It could be that 20 years of use have just taken their toll and it just plain wore out from metal fatigue.
It now works good, not perfect, as it kind of judders halfway up, as if sticking on the sides. I sprayed silicone into the side tracks, but it didn't help. However, it goes up without any 'clunk', and goes down smooth as, well, glass.
My thanks to all again for the input. All the mounting bolts were tight, and for some reason, my model doesn't appear to have the down-stop adjustment pictured in the MB manual. That wasn't my issue anyway, but I thought I'd mention this, since someone might suggest adjusting to stop the juddering.

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1986 560SL
2002 Toyota Camry
1993 Lexus