Step 1: Preheat oven to 350 and line 2 cupcake/muffin pans with paper liners.
Step 2: In a small bowl or measuring cup, whisk together cocoa powder and hot water until smooth. In a medium bowl, whisk together flour, baking soda, baking powder, and salt.
Step 3: In a medium saucepan over medium heat, stir together butter and sugar. Heat, stirring occasionally, until the butter is melted and the mixture is smooth. Transfer to the bowl of a stand mixer or a large mixing bowl, and beat until the mixture is cool, 4-5 minutes. Add eggs one at a time, mixing well after each addition. Add vanilla and cocoa mixture, and blend until smooth. With the mixture on low speed, add the flour mixture in three additions, alternating with the sour cream. Mix until smooth.
Step 4: Scoop into prepared pans, filling 2/3 full.
Step 5: Bake until a toothpick comes out clean, about 15-18 minutes. Let cool.
Step 6: Whisk together the flour and the milk. Heat in a small sauce pan on medium heat. Whisk continuously until it starts to thicken. Let it cook, while stirring with a rubber spatula, until you can start to see the bottom of the pan. Continue to cook until the mixture has the consistency of thick pudding or paste. Put mixture in the fridge and let it cool completely, stirring occasionally.
Step 7: It an electric stand mixer, beat the butter and the sugar using the whisk attachment for a minute or two until well combined and fluffy. While beating, add in the flour mixture and the vanilla. Beat to combine and then scrape down the sides. Continue beating until mixture comes together and is light and fluffy (about 7-8 minutes).
Step 8: Mix all ingredients together in a microwave safe bowl. Heat at 50% power for one minute, then stir. Continue heating at 50% power for 30 second intervals, stirring between each interval, until melted and smooth.
Step 9: Place powdered sugar in a small bowl. Whisk in milk until icing has a consistency that can be easily piped while still retaining its shape.
Step 10: Prepare the frosting and ganache while the cupcakes are cooling. When the cupcakes have cooled completely, fill each cupcake with a small amount of filling. I put the filling in a pastry bag with a round tip, inserted it into the cupcake, and pushed filling in until the cupcake started to plump up. You could also cut out a small circle in the center of the cupcake, spoon in some filling, and replace the circle. When the cupcakes have been filled, dip each cupcake into the bowl of ganache, covering the entire surface. If your ganache cools down too much to handle easily, microwave it for 15-30 seconds on 50% power. Let cool and then pipe designs on the top using the icing.
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