Preheat the oven to 350°F (175°C). Line a cupcake pan with cupcake liners. In a bowl, whisk together the flour, sugars, cocoa powder, baking powder, baking soda, and salt.
In another bowl, mix the eggs, milk, oil, vanilla extract, and sour cream until smooth. Combine the wet and dry ingredients and stir until smooth. Gradually add the boiling water, mixing to a thin batter.
Divide the batter evenly among the cupcake liners, filling them halfway. Bake for 18-20 minutes or until a toothpick inserted into the center comes out clean. Let the cupcakes cool completely.
For the coconut-pecan frosting, combine evaporated milk, sugar, butter, and egg yolks in a saucepan. Cook on medium heat, stirring constantly until thickened, about 10-12 minutes. Stir in vanilla, coconut, and pecans. Cool.
For the chocolate frosting, beat melted chocolate, butter, powdered sugar, cocoa powder, cream, vanilla extract, and salt until smooth. Add extra cream if needed to reach desired consistency.
Once cupcakes are cooled, frost them with the coconut-pecan mixture and then top with chocolate frosting. Serve and enjoy!