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I have this exact same problem on my2012 800r xmr and after checking everything over I determined the the inner sheave bushing on the secondary was worn out. This will cause the helix to wear and eventually break. These 2 parts are available aftermarket. This will fix your hard shift problem.

it does sound like a loose battery connection, seen that happen as you described many times

Since all the lights went off when it made the clunk noise and didn't start, it means the voltage dropped very low, which is why the starter didn't work, and since it started two hours later the battery can't have been flat, so it must have a bad connection somewhere. You should check the battery cables and the smaller wires going to the fuses and switches are tight everywhere, on the battery, on the body or engine, positive and negative. The battery cables, and wires, can get bad contact where the wire crimps into the metal terminals as well, and to find that you can inspect them, and wriggle them, and/or do what's known as a "voltage drop test". To do the voltage drop test you attach a volt gauge from one end of the cable/wire to the other end of the cable you want to test, and when you press the start button that gauge should stay reading zero volts. If it shows a voltage when you are pressing the start button then it's because there's a bad connection somewhere and some of the power is going through the gauge. Because the bad connection might be in the crimped terminal or the connection between the terminal and the bolt it's attached to though you need the gauge right on the bolt/engine/starter solenoid stud, and right on the battery post. It's also possibly a bad/dirty switch, either key or kill switch. To do a voltage drop test across them you attach the gauge with the key/switch off and it will show battery voltage, but when you turn the switch on it should bypass all the power going through the gauge and the voltage should drop to zero then.

Clean primary clutch "one way bearing" pin+spring unit = That is between plate's... When it start to stuck = You loose "neutral".. It will get really hard to "shift".. I'm working with brp stuff Transmission oil would not stuck chance really easy...

Check out this chart for example https://www.atvwheelsize.com/tech/atv-wheel-size-explained.html You can check what size tire you can buy for this wheel