Is this normal gear whine for an old KZ1000 Police

Not that I saw and I did look. The previous owner did say the oil was pretty dirty so he changed it. Before that the bike was sitting. He drove it for a while afterward. I pulled the pan for that extra step but did not see anything, just some bits of old gasket. . I'll pull the clutch side tomorrow. If a bearing on the input shaft is bad, should I be able to feel it with the clutch basket off?

That's rarley the case. I suspect he was in there and didn't tighten the nut properly. You can hold the break while tightening the nut. Some say you can't reuse it but I use blue Lock Tight with no problems. Torque it to spec.
Steve

will this tool help? I used it to torque the rotor. The brake could not hold the crank pulling off the alternator rotor, (I even had my wife sit on the bike while holding the rear brake) but the tool helped me spin the alternator rotor on and off. I'm hoping to re-torque it on the clutch side tomorrow.

I borrowed this tool (way cool) and I may have to buy one! Its a kent-moore Yamaha snowmobile tool YS-1880-A, for those who cant get the factory clutch tool (or use a penny to jam the gears?)

There's a special tool for holding the clutch basket from moving when removing / installing the clutch hub nut. It is not anything very fancy (see images below). You can make one easily enough if you have 2 extra steel clutch plates and someone with rudimentary welding skills. Ed

Here is a video of the loose clutch before I took it apart. I would have thought it not be so loose, but after taking it apart, it does look like it's designed to float some. Is this normal?

Here is a video of the bike running with the entire clutch basket and ring gear removed. I put the clutch cover back on and the oil, so I could see if the noise went away. Am I nuts or does it sound exactly the same?

So you ran it with no basket in it? Was the nut loose? Put it all back together with the not tight and see if it goes away. You might have to split the cases.
Steve

I don't get the angry eyes? What did I do wrong? I did not run it without oil. and with no clutch and ring gear, the noise was unchanged, and yes, the nut was tight before then. That should rule out the transmission and clutch.

Yes, I'm guessing for a quiet running motor, one will have to split the cases. Who knows how much wear is in this engine. Seems to have been running this way for a few years per the P.O.

You can split the cases without pulling the head. Should have told us it's been like this with the Po. Hopefully the gear on the crank isn't damaged. Should be able to find a tranny at The Old Kaw Man. I've gotten good parts from him. Buy the set.
Steve