Scott,
I used some bath and kitchen type sealant that can be cleaned up with water. I CARFULLY injected a small bead around the perimeter, and then wiped most of it away with paper towels/rags. I finished the process by wiping the area with a damp sponge cleaned often with water until all of the sealant residue was removed.
Yeah the gasket punch sure did work for cutting the rubber. I tested drilling the holes, and don't think it would have worked as well. I don't know about you, but I was glad to have the rear window task behind me.
Paul