I finally figured out how to stop my one endlink from clunking after swapping my sway bar and endlinks on the GTI. I spent the last few days trying to figure out what I needed to do differently, worried that the stiff setting was putting the endlink at too much of an angle to function correctly, and was about to take everything apart again, which I was not looking forward to.
It was only clunking under significant offset bumps or sharp corners, with the central ring of the endlink probably hanging up on the opening in the control arm. While the bolt holding it to the control arm appeared to already be tighter than the one on the other side, it turned out that it needed more tightening (after I tried loosening it first).
I am drafting a detailed report on my swap with photos that may help one or two others who may someday do this, and now I have the satisfactory ending.