Combine all three ingredients for the ganache filling in a bowl. Double boil the chocolate mixture, whisking until smooth. Remove from the double boiler and chill in the refrigerator for no more than 25 minutes.
Chocolate Cupcakes
Mix the bittersweet chocolate with the cocoa powder in a bowl. In a cup, combine 3/4 cup of hot water with the instant coffee powder. Slowly add the coffee to the chocolate mixture and whisk until smooth. Chill in the refrigerator for 20 minutes.
Preheat the oven to 350°F (176°C). Sift the bread flour, sugar, salt, and baking soda into a bowl. Set aside.
Use a new bowl to beat together the oil, eggs, white vinegar, and vanilla extract. Slowly add the chocolate-coffee mixture and whisk well.
Next, add the sifted ingredients in 2–3 tablespoon increments, whisking until smooth. Divide the batter evenly among the cupcake liners. Drop a rounded teaspoon of the ganache filling into the center of each cupcake batter. Bake the cupcakes for 15–18 minutes, or until firm to the touch.
Vanilla Buttercream Frosting
Using a mixer with a paddle attachment, beat the butter until soft and fluffy at medium speed. Slowly add 3 cups of confectioners' sugar, 1 cup at a time, mixing well after each addition. Then, add the vanilla extract and 1 tablespoon of heavy cream, and continue mixing for another 2–3 minutes.
Adjust the icing stiffness as needed. Add an additional tablespoon of heavy cream if the icing is too stiff, or 1/2 cup of confectioners' sugar if it is too thin.
Notes
Alternate method to melt the Ganache Filling is to use the microwave. Combine all ingredients in a microwave-safe bowl and heat on high for 20-30 seconds. Whisk until smooth. Chill in the refrigerator for no longer than 25 minutes.