Ball bearings falling out

Yeah, I totally understand that. Nothing sucks more than working your butt off to fix something, and then having it remain unfixed.
I'm still racking my brain trying to think of where such a small ball bearing would come from.

You just swapped from 318 to 340 - did you confirm your crank is drilled deep enough for the input shaft? Should be, I would guess.

How's the oil pressure on the 340? Was it recently rebuilt? A bad thrust bearing can cause a loss of oil pressure but could also maybe cause an issue when you press the clutch pedal down. Just spit balling here...