he pins are threaded in. No don't go in to the water jacket. The biggest problem might be getting them, use some penetrant, and a big pair of vice grips. You need to remove them to get good even pressure on the gasket. Double check the header flange make sure that it is flat, none of the welds higher than the others. Consider double gaskets and the copper RTV in between.

Larry

I don't own a vehicle that isn't old enough to drink.