So when you were kicking, it felt like the piston/crank was locking up occasionally? But once you took off the cylinder to check you found no problems there? Did you try to carefully push down the kick when you had the cylinder off? And was it still locking up?
Check the alternator to make sure it is turning freely.
If there are no issues on the alternator side, then your problem could be with the kicker itself, with the clutch or the two small gears on the clutch side.
It could also be a gearbox issue. How easy is it to put the bike in to neutral? And can you go through all gears while the motor is not running (I assume that your are not able to start the bike currently).
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