Place the chocolate and cream in a medium microwave-safe bowl and microwave until mixture is warmed, about 30 seconds. Whisk until smooth. Place mixture in refrigerator until just chilled and firmed, no longer than 30 minutes.

Meanwhile, preheat oven to 350°F.

In a medium heatproof bowl add the chocolate and cocoa. Pour hot water over mixture. Cover and let stand for 5 minutes. Whisk mixture gently until smooth then set aside to cool.

Line a standard 12-cup muffin tin with foil or paper liners.

In a small bowl, whisk together the flour, sugar, salt, and baking soda.

Whisk sour cream, oil, eggs, egg yolk, vinegar, and vanilla into the cooled chocolate mixture until smooth. Stir in the flour mixture until smooth, being careful not to overmix.

Using a spring-loaded scoop, divide the batter evenly among prepared muffin cups. Bake until cupcakes are set and firm to the touch, about 17 to 20 minutes. Let cupcakes cool in pan on a wire rack for 10 minutes before removing from pan to cool completely, about 1 hour. Cupcakes can be stored in an airtight container at room temperature for up to 1 day.

Using an apple corer or pairing knife, slice a small section of the center of the cupcake, being careful not to slice through the bottom. Fill each hole with 1 heaping teaspoon of the firmed ganache.

In the bowl of a stand mixer fitted with the paddle attachment, mix together the sugar, cocoa powder, and butter. Mix on low speed until well blended and then increase the speed to medium and beat for another 3 minutes. Add the salt, vanilla, cream, and cooled melted chocolate and beat on medium for 2 minutes, or until light and fluffy.

Spread or pipe evenly over filled cupcakes. Serve or store covered at room temperature for up to 1 day, or covered in the fridge for up to 3 days.