I don't have a duplicator and always had trouble making plugs with the same amount of blank left over so I could do the rest of the drilling in a jig.
Then I had a thought and it works.
Put a piece of masking tape on the face of the tool rest, you can mark the ends of the plugs, and anything else you want to locate on the tape. Then just use your skew chisel to mark the ends, the joint in a jointed or a pencil to mark hook and weight locations.