Heat oven to 350º with oven rack in middle of oven. Line a 12-cup muffin tin with paper liners.
Place flour, sugar, baking powder, and salt in a large mixing bowl and use a mixer fitted with a paddle attachment to mix them together.
With mixer on medium speed, add butter, sour cream. egg, egg yolks, and vanilla. Beat for 30 seconds, until smooth and satiny.
Remove mixing bowl from mixer and using a rubber spatula, scrape down the sides of the bowl and make sure batter is mixed evenly.
Divide batter equally among muffin cups and bake for 18 to 22 minutes. Let cool before proceeding.
Using a spoon or your fingers, create a hollowed out portion in each cupcake like you would to make a bread bowl, but being careful to leave a layer of cupcake all the way across the bottom.
Sprinkle some vanilla wafer crumbs at the bottom of each cupcake “bowl”.
Using an electric mixer, beat together the cream cheese and sweetened condensed milk for 2-3 minutes. Scrape down sides of bowl at least once.
Add milk, vanilla extract, and pudding mix and beat until mixed together well. Stir in bananas by hand. Immediately spoon into cupcakes.
Spoon pudding mixture into the holes with enough extra so you can create a layer of pudding spread across the top of the cupcake.
Use an offset spatula or a pastry bag fitted with a large tip to add whipped topping on top of the pudding mixture. Garnish with a whole vanilla wafer and more crumbs if desired.