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Maybe one of the timing chains is bunching up on one side. Make sure both chains are hang about the same length and motor is sitting level. My other guess, without seeing a photo is what 356RS said, flywheel catching on something as simple as a bolt holding the yoke in place. Maybe you can provide a few photos from different ends. Maybe we'll see something you don't. If for some reason you have one or all pistons removed, the con rods are catching at rotation points within the case.
Regards, R
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