I found the distinct signs of pre-goats in my 2006 GS500F and have since been working on it on and off. I replaced the goats-induced generator rotor and the larger gear in the starter clutch set (hiding behind new generator rotor in the attached picture). I won't go into why I replaced that larger gear because it's a long story. The problem is characterized by the loud, high pitched noises in the video. Bike also idles rough before stalling out. It may be related but took off the signal generator cover to find the 2 electrical contacts on the signal generator have signs of overheating - the plastic around them is burnt and cracking.

I'm newer at this so excuse me if this thought makes anyone want to slap me but maybe I threw off the timing by installing the new big starter clutch gear improperly?

Sounds like it's time for a new fan belt!  LOL!

It definitely sounds like a rub though.  No idea what might be capable of making such a noise though.

Welp.. After the bike stalled I inspected more, tried starting it again just to hear a single "tock" each time I hit the ignition. Eventually I landed at the starter and so I took it apart. It was damaged inside - some black goop, broken copper windings and other burnt components. I then looked at the spark plugs and they are wayyy blacker than they should be at only 3,000 miles put on them. Pitch black so I replaced them today.
My gut is telling me that the starter failing and black spark plugs are not the problem, but merely frustrating symptoms.