On the gears, if the teeth on one of the gears was somehow damaged you'd have the issue accelerating and decelerating, and if maybe the dogs were damaged the slip when they disengaged and engaged again would be (from what I can tell from the video) a lot more violent and probably something you could hear.
the_gooch is probably on the right track with it being a clutch issue, though I'm guessing he's talking about worn clutch plates? It's a little bit hard to tell in the video, does the engine speed change with the jerk? Any tight spots in the chain? Wheels rotate relatively freely/smoothly with the bike on stands? I know it's harder to test this, but is there any semblance of this issue in the higher gears?