Preheat your oven to 350°F and position the rack in the middle. Line a muffin pan with cupcake liners to make for easy removal after baking.
In a microwave-safe bowl, combine 1 stick of unsalted butter and 8 tablespoons of semi-sweet baking chocolate. Melt them together in 30-second increments, stirring after each interval until smooth. Let it cool to room temperature.
In a separate bowl, sift together 3/4 cup of unsweetened cocoa powder, 3/4 cup of all-purpose flour, 1/2 teaspoon of baking soda, 1 teaspoon of baking powder, and 1/4 teaspoon of salt. Set this dry mixture aside.
In a stand mixer fitted with the whisk attachment, combine 2 large eggs, 3/4 cup granulated sugar, 1 teaspoon vanilla bean paste, and 1/2 cup sour cream. Whisk on medium speed until the mixture is smooth and creamy, about 1 minute.
Once your melted chocolate and butter mixture has cooled, add it to the egg mixture and whisk until fully incorporated, about 30 seconds.
With the mixer on low speed, gradually add the dry flour mixture to the wet batter, about 1/4 cup at a time. Mix until just combined to avoid over-mixing, which could make the cupcakes dense.
The batter should appear thick and shiny. If needed, use a spatula to ensure everything is well mixed.
Carefully fill each cupcake liner about two-thirds full with the batter, which allows room for the cupcakes to rise without overflowing.
Bake the cupcakes in your preheated oven for 15 to 18 minutes. Check for doneness at the 15-minute mark; they should spring back when gently pressed in the center.
While the cupcakes bake, prepare the filling. In a saucepan, combine 1 cup evaporated milk, 4 large egg yolks, 1 cup light brown sugar, and 1 stick unsalted butter. Cook over medium heat, stirring continuously until the mixture thickens and comes to a light boil, about 10 to 15 minutes.
Remove the filling from heat and strain it into a bowl using a fine-mesh strainer. Stir in 1 teaspoon vanilla extract, 2 cups sweetened shredded coconut flakes, and 1½ cups chopped pecans. Let it cool to room temperature.
Once the cupcakes are baked and cooled to room temperature, use a sharp knife to cut a small cone from the center of each cupcake and remove the tip. Fill each cupcake center with the coconut-pecan filling.
To make the frosting, melt 12 oz semi-sweet chocolate in a microwave-safe bowl, then set aside to cool slightly. In a stand mixer, cream together 3 sticks unsalted butter and 8 oz cream cheese until fluffy and pale yellow.
Add the melted chocolate to the butter mixture and beat until combined. Gradually add 2 cups confectioners’ sugar and 1/2 cup unsweetened cocoa powder, mixing on low until incorporated, then beat on high for 1 to 2 minutes until fluffy. Adjust the consistency with whole milk as needed.
Frost each filled cupcake as desired, creating a beautiful dome of frosting on top.
Refrigerate the frosted cupcakes for 30 to 40 minutes before adding the chocolate ganache. To prepare the ganache, heat 1/2 cup heavy whipping cream in the microwave until hot, then pour it over 4 oz chopped semi-sweet chocolate in a bowl. Let it sit for 2 minutes and stir until smooth.
Allow the ganache to cool to room temperature before drizzling it over the frosted cupcakes. Garnish with 2 tablespoons of unsweetened shredded coconut flakes, and your German Chocolate Cupcakes are ready to serve!
