I've mentioned this before, but will bring it up again.
The syncopated beat of this engine, which sounds so neat, is because the engine "fires" twice in one revolution then skips one entire revolution. This makes equalizing the air pressure to both cylinders very difficult.
The amount of air pressure that builds up in the line is greater during the skipped revolution than between the two firings. This results in one cylinder hitting "harder" than the second. You can mitigate this affect somewhat by adjusting the lead cylinder rocker arm clearance to a thicker setting so the valve doesn't open as far or stay open as long.
From the video, it kind of looks like you may have already done this.
Chuck