I've never installed ship lap flooring, but you could still use a flooring stapler on the "tongue" of the planks. I would use a quarter inch bead of the best poly-urethane flooring glue that comes in a sausage that uses a special gun to dispense the glue. You would then only need to top-nail one side of the planks on the edge where you are going to top-nail, usually about every foot along the board. I would recommend 8d casing nails instead of 18 ga. air nails. The finish nailer does not pull the planks down, it will only hold the plank as it as when the trigger is pulled. If you do prefer to use a finish nailer, it would help to step down, placing a lot of weight on the spot where you nail, each time you pull the trigger. Some people double nail each time when using the finish nailer, "toe-nailing" both nails, placed at opposite angles, to help hold the plank as the glue hardens.
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