I just now got to watch that video: I see the wiggling Neutral Switch!
That IS odd. It indicates that somewhere in the tranny, some gear's dogs are clicking across the neighboring gears' slots, being too close to each other for Neutral to happen.
When this happens in the CB750 (most commonly 2nd gear) it is due to a bent "L" shift fork, which happens when the bike falls over to the left and something hits the shifter, pushing it upward without the engine running. Then the weight of the bike on the shifter arm screws the shift drum into the "L" forks' dog and moves the C2 gear hard against the C5 gear: without the engine running the dogs don't find slots and the sheer weight of the bike bends the shift fork tines sideways, moving the C2 gear off its normal disengaged position when not being used.
While this happens much more rarely on the lighter CB500/550, it does happen, and there will be a witness mark on the upper side of the tunnel where the shift shaft enters the engine below the drive sprocket. Sometimes the shift shaft gets bent slightly upward, too. This then puts a 'bias' against the shift drum, turning it slightly when in the unused position. That can sometimes cause the shift drum to turn ever-so-slightly off the "in between gears" Neutral position, which nudges gears C1 and M1 toward their neighbors in the gearbox. Then they 'click' against one another when the engine turns.
So, maybe put on the Sherlock Holmes hat & find a pipe to chew on (don't smoke around gas! I've done that...) and look for clues on the shifter arm, its shaft, or even on the (internal) shift arm ratchet parts to see if something is bent that is nudging the gears away from their Neutral positions. Inside the transmission, the tips of the dogs on a gear are tapping against the neighboring gear because the shift drum is not exactly in the Neutral spot. Something in the shift mechanism would be my best guess?