The top cylinder is the one that is firing erratically and running poorly. The bottom cylinder is running normally from what I see in the video. I'm still feeling like this is an ignition problem. Either a bad coil or condenser seems most likely to me. I'd start with a condenser since that is the easiest thing to swap. If no difference, try a new coil, and wire. One other thing, have you tried swapping the spark plugs from top to bottom to see if the problem follows the plug?
If none of those things do it, maybe check behind the exhaust cover and make sure it isn't sucking water into the top cylinder somewhere.
YouTube handle: Old JohnnyRude