The smaller hole on the header portion is in a position for an effective muffler tap to provide pressure to the fuel tank if you choose to use it that is where I would locate such.

The larger hole is centered to the outlet pipes and likely an intended point for smoke oil injection to provide uniform smoke from both outlets. If you have no smoke then plug the hole.

Do not plumb the crankcase vent to the muffler, leave it open to atmosphere or just a length of fuel line to clear the cowling if you like.

John