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To prepare cupcakes: Preheat oven to 350°F. Line 12 (1/2-cup) muffin cups with paper liners.
Whisk whole-wheat flour, cake flour, baking soda and 1/2 teaspoon salt in a medium bowl.
Beat granulated sugar and oil in a large mixing bowl with an electric mixer on medium speed until combined. Scrape the black paste out of the vanilla bean into the sugar mixture. Add applesauce, egg, egg yolk and vanilla extract and beat until well combined. With the mixer on low, alternately mix in the dry ingredients and 1/2 cup evaporated milk, starting and ending with dry ingredients and scraping the sides of the bowl as needed, until just combined. Divide the batter among the prepared cups (they will be full).
Bake the cupcakes until a toothpick inserted into the center comes out clean, 20 to 22 minutes. Transfer to a wire rack and let cool completely.
To prepare frosting: Meanwhile, whisk 2/3 cup of the remaining evaporated milk, all-purpose flour and a pinch of salt in a small saucepan until no flour lumps remain. Cook over medium heat, whisking constantly, until it looks like a thick, stiff paste, 2 to 5 minutes. Remove from the heat and continue whisking for about 30 seconds to cool slightly. Whisk in chocolate until completely melted. Transfer to a medium bowl. Add confectioners’ sugar, cocoa and vanilla and beat with an electric mixer until smooth and creamy. Refrigerate the frosting until thickened and cold, about 2 hours. Spread the frosting on the cooled cupcakes and decorate with sprinkles, if desired.