So the sporadic clunking I could feel / hear in the drive train was definitely due to the rear wheel / motor. Mine developed a bad bearing which made a terrible racket (I don't think this was related to the clunking - totally different noises, and the occasional clunking was there from day 1, and the bearing racket was extremely obvious and developed only at about the 140 mile mark).
Juiced sent a new rear wheel / motor, and I wanted to use it a while before reporting back, but that clunking that came and went is 100% gone. This after putting almost 100 miles on the new motor / wheel.