it looks like somethings got in between things, like a bolt or some thing when the gearbox has been moving and as its dragged it round its broke where its been weak
or a spacer.shim in the wrong place on installation and as the cases have bin tightened together its broke the case
all inturnals are hardened steel and the cases are soft alloy the alloy will fail b4 any of the drive train
I still haven't disassembled the engine(the pic is from a friend that have the same problem).What i have noticed is that the original bearing that yamaha gives for the shaft has something like a spacer on it and mine that is changed doesn't have that,so maybe the crank gear wasn't working right with the clutch and that caused that.On the other hand maybe something go wrong in the gearbox.