Preheat the oven to 325 degrees F. Line 2 muffin pans with cupcake liners.
In a medium bowl, sift together the flour, cocoa powder, baking soda, baking powder and salt. Set aside.
Place the chopped chocolate in a small heat-safe bowl and pour the boiling water over it. Whisk until the chocolate is melted, and then let it cool for 15 minutes.
In a small bowl or large measuring cup, combine the buttermilk and vanilla extract. Set aside.
In the bowl of a stand mixer with the whisk attachment, whisk the eggs on high speed until foamy, about 2 minutes. Reduce the speed to low and slowly pour in the oil, whisking until it is combined, about 30 seconds. Next, slowly pour in the cooled, melted chocolate. Add the buttermilk mixture, and then pour in the granulated sugar and whisk the batter until it is smooth and liquid, about 2 minutes. Stop the mixer, remove the bowl and add the sifted dry ingredients. Mix by hand just until the dry ingredients are incorporated, lifting and folding in from the bottom center. Using a rubber spatula, scrape down the sides of the bowl and mix again just briefly; the batter will look very lumpy, but stop mixing. Pour the batter through a medium-mesh sieve into a large bowl to remove any lumps. Press against the batter in the sieve with the spatula to push through as much batter as possible.
Fill the cupcake liners half full with batter and bake until a wooden toothpick inserted in the center comes out clean, 20 to 25 minutes. Transfer the pans to wire racks to cool completely before filling and frosting.
To assemble: Core the center of each cooled cupcake using an apple corer. Place the cooled, thickened Dark Chocolate Ganache in a pastry bag. Cut a small bit off the bottom of the bag and fill each cupcake by inserting the tip of the pastry bag into the cored cupcake. Generously frost the top of each cupcake with the Chocolate Mascarpone Frosting.
Place the chocolate chips in a heat-safe bowl. In a small saucepan, heat the heavy cream until you see tiny bubbles around the edges. Pour the heavy cream over the chocolate and leave it alone for 5 to 10 minutes. Add the butter and vanilla extract to the melted chocolate and whisk everything together until it has a smooth consistency. Let the ganache cool to room temperature; the ganache will thicken upon standing.
In the bowl of a stand mixer with the paddle attachment, combine the mascarpone cheese, cocoa powder, butter and vanilla extract. Beat on medium speed until smooth. Gradually add 2 cups of the powdered sugar, beating well. Beat in the milk. Scrape down the sides of the bowl, and then gradually beat in the remaining powdered sugar. If necessary, beat in additional milk, 1 teaspoon at a time, to reach desired consistency.
This recipe was created by a contestant during a cooking competition. It has not been tested for home use.