Preheat the oven to 350 degrees F. Line regular sized cupcake pans with 24 liners.
Sift the flour, sugar, cocoa, baking soda, baking powder, and salt in a mixing bowl fitted with a paddle attachment.
Mix on low until incorporated, about 30 seconds.
In a separate bowl, combine the egg yolks, egg whites, milk, oil, water, and vanilla.
Add the liquids to the dry ingredients in 3 stages, scraping down at each addition and beating for about 30 seconds.
Fill the cupcake liners three-quarters full and bake until baked through, 18 to 20 minutes. Cool completely.
Fill a piping bag with the slightly chilled Chocolate Ganache.
Cut the tip of the bag off and insert the tip into the center of a cooled cupcake. Squeeze to allow a small amount of mixture into the center. Release and remove the bag from the cupcake. Repeat on the other cupcakes. Generously frost the top of each cupcake with Peanut Butter Cream Frosting.
Drizzle with remaining Chocolate Ganache.
In a mixing bowl fitted with the paddle attachment, beat the butter and cream cheese. Scrape down the bowl and beat until smooth, about 2 minutes. Scrape down the bowl again and add the peanut butter.
Mix until blended. Scrape down again and add the confectioners' sugar and vanilla.
Mix until incorporated.
In a microwave-safe glass bowl, heat the heavy cream and butter for 1 to 2 minutes until mixture just bubbles.
Add the semisweet morsels.
Let stand for 1 minute. Stir constantly until dark, thick, and creamy. Slightly chill before using.
