In consultation with another, I would say that you haven't engaged the clutch lifter shaft with the clutch lifter rod.
All was good in there before you pulled this case off, nothing else has been un-bolted nor have you introduced anything new into this area.
So that leaves "Operator error" ?
But, I did not have the case off before now, so the scratches, if I did it, could only have happened as a result of my changing out the clutch cable -- Murphy at work -- if it can go wrong . . .