01 - Preheat oven to 350°F. Line a 12-cup muffin tin with cupcake liners.
02 - Whisk together flour, baking powder, and salt in a bowl. In a separate large bowl, cream butter and sugar until light and fluffy. Add eggs one at a time, beating well after each addition, then mix in vanilla. Add flour mixture in three additions, alternating with milk, beginning and ending with flour. Mix until just combined.
03 - Divide batter evenly among cupcake liners. Bake 18-20 minutes, or until a toothpick inserted in the center comes out clean. Let cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
04 - Heat milk in a saucepan over medium heat until just simmering. Whisk egg yolks, sugar, cornstarch, and salt until pale and smooth. Gradually whisk hot milk into yolk mixture. Pour mixture back into saucepan and cook over medium heat, whisking constantly, until thick and bubbling, about 2-3 minutes. Remove from heat; stir in vanilla and butter until smooth. Transfer to a bowl, press plastic wrap directly onto surface, and chill until cold.
05 - Heat cream in a small saucepan until just simmering. Pour over chocolate in a heatproof bowl. Let sit 2 minutes, then stir until smooth. Allow to cool until slightly thickened but still pourable.
06 - Using a small knife or cupcake corer, cut a small hole in the center of each cupcake about 1 inch deep. Fill each with chilled pastry cream, about 1-2 teaspoons per cupcake. Replace the cut-out piece of cake on top. Spoon or dip the tops of the cupcakes in chocolate ganache. Let set before serving.