I watched the 'first test ride' video - get rid of that helmet ! Pudding basin helmets have been responsible for a lot of deaths, and riding something like that, you have just got to wring its neck !
I wondered whether you have changed the balance factor of the crankshaft. The motor in my Seeley is rigidly mounted, and the crank is balanced to 72 % by filling a steel plug in the hole in the flywheel. When it is idling, the bike rocks back and forwards, but when revved it is as smooth as silk. The original commando was balanced at 58 %. If you rev them as standard, you can split the cases horizontally through the main bearings. Better that the bike shakes at low revs, than that happens.