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The 2 holes you've marked on the gearbox bearing areas are blank holes for the dowels which locate the bearings. A quick blow with an air gun will clear those I reckon, no need to blank them.
Dont forget the holes at the oil filter and oil pump plus the gallery where the blanking plug does behind the generator cover
Yes, a screwed in cap at points end and a plug with O ring held in by generator cover at other