Crankshaft shifted forward?
 

Jiris,

Glad to hear that you finally found the problem. Just wondering if you had taken the flywheel off for main seal replacement or something prior to finding the pieces in the sump. I haven't seen it first hand, but think that the kind of damage you describe can come from the crank accidentally moving forward and then things not aligning when the flywheel it put back on. For a rather intense discussion of this problem see Flywheel, removal warning, main seal, oil pump cover, oil pump . The article scared me enough that I made a little metal strap that held the front of the crank rearwards when recently replacing a rear main seal. It worked. Whew!

Don't know about how they balance them at the factory, but I just made sure I punched the crank, flywheel and clutch pieces so that it all went back together the same way I took them off. There were some faint paint marks from the factory on all pieces but I just ignored them and used my own marks.