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Ok, assuming you flattened out the bend washer, this is what I did to remove that nut from my 650 Versys (which had the tightest countershaft nut I ever encountered).

In my shed I had the bike held upright with tie down straps. No rear stand. I had the engine in neutral as I didn’t want to hammer the gears. (My 1/2 inch electric impact was useless).

To lock the rear wheel from spinning, I stepped hard on the rear brake then tied it down with tie-wire. Shoving a wooden board between the spokes will only serve to damage them.

Then I used a 1/2 inch breaker bar with a four foot long piece of pipe as a handle extension making the effective length of the breaker bar five feet long.

I got behind the bike (because there was more open space to work) and lifted with such force the rear wheel lifted off the floor nearly a foot.
With the rear wheel off the floor I let it drop a bit then pulsed up on the extension handle and…. BOOM! The freaking thing sounded like a rifle shot. I broke the countershaft itself, or at least I could have sworn I broke the countershaft. I did not. Whew!

After changing the sprocket I reinstalled the nut using the proper torque spec.

This was a common complaint on the 650 Versys forum I belonged to. Kawasaki way over tightened that nut at the factory. I rode it for years at the proper torque spec without issue.

If you use my method, you should get somebody to sit on the bike, in neutral, with both the front brake applied and a lot of rear brake. Their extra weight will help hold the bike down also.
 

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Well, update:

I took all the steps mentioned above, and some extra steps too. Put a cheater bar over my breaker bar and pressed down with all my strength. BANG! I thought I got it! Nope. Jokes on me. The damn nut rounded off. Like, all the way off.

So I'm out of ideas. Short of cutting it with a tungsten carbide burr, that nut is an integral part of the bike. I have wrestled seized bolts and nuts before, but absolutely nothing like this. I have a feeling the spindle wasn't dressed properly with moly or anti-seize. So through vibration and pressure, the nut is basically welded to the shaft.

Very, very frustrating.
Oops, shoulda mentioned… six point socket only.
You might still be able to get it off with a six point socket if you haven’t used one already. Also, the breaker bar/socket must be 90 degrees to the shaft/nut. If you have any other angle it'll peel off. I know you can get it square by lifting from the rear.
Some small amount of heat on the nut will help but you don’t want any heat on the shaft at all.

If you can’t bang a six point on (or a six point with shim stock) then a careful session with a cutoff wheel is your next step. Perhaps you could cut just partway (to stay away from the shaft threads) then more twisting with a socket will split the nut.
 

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Don’t forget to rebend the bend washer.
That Versys was the only new bike I ever encountered this over torqued nut on.

Also, I know you’re supposed to replace chain and sprockets together, which I normally do, but I’ve done just the chain before if the sprockets looked good and 12,000 miles later when I sold the bike, they still looked good.
I believe the rear sprocket on the Versys didn’t have an offset and could be reversed to get at the unworn part of the teeth. There was a member on the site that used to do it. The Ninja may be the same.
 

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Yup I'll bend it back just in case. The sprockets look fine for wear. I just wanted to upgrade to racing sprockets and do it with the chain. But it's okay. Not the end of the world.

I have had 4 different bikes over the years, 3 of those were dirt. But I've never seen a nut seize like this one. The KTM was really tight but nothing like this.

I figured well, now this bike has a lifespan haha. It'll be crushed and recycled with that forsaken nut still attached! (That's a joke, I'll cut it off before I scrap this bike)
Probably grinding it down to near the threads is best. Then I’m sure a socket will twist It off.
 

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Yeah, I've done the same with dirt bikes. I wanted to do the whole package on this Ninja because it sat for 10-odd years in storage and I have no clue how it was treated by the first or second owner. It looks fine, but I dunno! Just wanted to do the whole thing. But after that struggle with the nut, I'm just gonna leave it be!

I strung a new Vortex chain over a new Vortex rear sprocket. Should be fine with that!
The front sprocket (not sure about rear) will be case hardened so with frequent chain lubrication it’ll last.
That 650 engine is nice, ample power for the street and reliable. The cool thing about it is that it has a cassette style gearbox. You can actually pull the gearbox out of the engine without splitting the cases while leaving the engine in the frame! That’s motoGP type stuff. I don’t know of any other street bike that has one. Certainly not a budget bike.
So if someday you break the countershaft… no biggie.
 

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I actually didn't know that! That is awesome! Yeah I love this engine, smooth and powerful for what it is.

Only weird thing is that going from neutral to first, it clunks really hard. But I've read (I think on this forum) that it's a kawasaki thing and not to worry about it.
My Kawi ZRX1200 clunks heavily going from neutral to first. So what I do is pull the clutch and hold it for ten seconds while I pedal the bike forward to get all the gears moving, then I shift to first gear and there’s no clunk at all. Try that with the Ninja.
I don’t remember my Versys doing it. My 2017 z900 doesn’t really do it but I’m in the habit of pedaling forward on all my bikes including my zr7S, just a slight push forward with your feet, It’s easy and becomes second nature. That big clunk isn’t good for the gearbox. Excessive chain slack can cause it as well.
 

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I used the proper mm SIX POINT socket and pulled up from the rear to keep the socket square to the nut. There was no slipping on the nut. The problem was excessive torque, which my four foot cheater bar overcame.
A twelve point socket would have slipped. Ever wonder why all impact sockets are six point sockets? (Hint: twelve point sockets slip).
 
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