Combine milk, sugar, flour, and salt in a saucepan over medium heat. Cook and stir until mixture thickens, about 5 minutes.
Beat egg yolks slightly in a bowl; add slowly to milk mixture. Stir constantly and cook until thickened, about 3 minutes. Remove from heat, add vanilla, and stir. Chill pastry cream until ready to use.
Preheat oven to 350 degrees F (175 degrees C). Spray a 9x13-inch baking pan with cooking spray.
Cover the bottom of the baking pan with a thin layer of pastry cream. Add waffles and cover with another thin layer of pastry cream.
Mix blueberries and strawberries together in a bowl. Sprinkle half of the berry mixture on top of the cream-covered waffles. Top with a layer of pancakes; spread remaining pastry cream on top. Finish with the remaining berry mixture.
Bake in the preheated oven until heated through, about 20 minutes.