Now that the gunwales and deck beams are mating up flush, you are ready to dowel them firmly in place.
Each deck beam is currently held in place by 4 nails. Remove one nail, drill a 15/64 inch hole through the gunwale into the deck beam 2-1/4 inches deep and drive a quarter inch dowel into the hole until it bottoms out. Drill the holes so they come in at a slight angle in the horizontal plane. Then remove the next nail, drill and dowel and so on until you have replaced all 4 nails with dowels.