FWIW, my $0.02 on the driveline lash.
Firstly, I feel better calling it a thunk than a clunk. It's omnipresent, but it never feels harmful. Only time will tell how the transmission holds up, but I think the cush drive is performing admirably. And for the record, my BMW GS has the exact same thunk, but it feels a little less severe because it's one noisy, vibrating mess.
Secondly, as a experienced motorcyclist, I can easily explain it away as standard driveline lash that's made way more apparent because of the way the clutch is used on this bike.
A) Off the line, you don't use the clutch and so it will thunk. Thanks a ton to someone (Richard230?) for mentioning the rollback at a light. I naturally do this anyway because I always come in hot at stops and the fork usually pushes me back when it extends a good deal.
B) Up shifting, you usually release the clutch with no throttle input because even the slightest input will spin up the motor when no under load. Consequently, the engine braking kicks in before you can get back on the throttle. I found that with some practice, I was able to smooth out the upshifts by slipping the clutch a little and barely rolling on the throttle at the right time. At first I was afraid of blipping the throttle too much and burning up the clutch when I engaged it at a motor RPM that was too high. But then I realized, that this is perfectly safe because it's not like the clutch is stopping a metric ton of rotating mass at a high RPM. There is very low rotation mass in this motor.
C) Slow speed maneuvering doesn't require the clutch, and so the thunk is worsened. Some mentioned (again Richard230?) dragging the brake while keeping the throttle open slightly. It does this trick, but it's not really my style. Instead I just try to roll on really slowly. It still thunks, but I'm really not too worried about it.
I guess my final thoughts are that this is a new experience for riders of both ICE bikes and direct-drive electric bikes. It just takes a little getting used to. Now I just hope I remember to pull in the clutch at a stop the next time a drive my GS. DOH!