Line the bottom of a 9x13-inch baking dish with Nilla wafers, breaking them to fill in any big gaps along the edges.
Whisk together 1 box of instant pudding with 2 cups of the milk for 5 minutes, or until the pudding thickens and appears set. Stir in 1 can of the crushed pineapple. Pour the pudding evenly over the layer of Nilla wafers, using a rubber spatula to spread into an even layer.
Top with another layer of Nilla wafers, again breaking them into pieces if needed to fill any large gaps.
Prepare the second box of pudding as you did the first, with the remaining 2 cups of milk. Stir the second can of drained crushed pineapple into the pudding. Pour the pudding over the 2nd layer of Nilla wafers, spreading it into an even layer with a rubber spatula.
Top with the Cool Whip, using a spatula to spread into an even layer. Refrigerate for at least 4 hours. Prior to serving, garnish the top with additional crushed Nilla wafers.