Bad vibrations
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@dtluke Inside the gearbox next to the primary shaft and the crankshaft, that odly shaped item is the balancer shafter. It harmonically dampens the engine. It is locked into place by the crank shaft. The crank to shaft is pulled to tdc, and two dots meet at their circumference.
If you don't, the engine will be out of nalance and will demolish the mains and gearbox.
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@Calum Cheer mate! You were spot on. Took it apart again. Lined everything up and just went out for a ride and she's better than even. first proper engine rebuild and it seems to have gone pretty well minus a few hiccups. Next one will be super smooth now.