Prepare the Cupcakes: Preheat oven to 350°F. Line 2 (12-cup) standard-size muffin pans with paper liners; set aside. Prepare cake batter according to package directions. Divide batter evenly between prepared muffin cups. Bake cupcakes in preheated oven according to package directions until a wooden pick inserted in center comes out clean, 15 to 20 minutes. Leave cupcakes in trays for 5 minutes before transferring to a wire rack to cool completely, about 30 minutes.

Prepare the Coconut Custard: Stir together brown sugar, granulated sugar, butter, eggs, and evaporated milk in a medium saucepan over medium. Cook, stirring constantly using a rubber spatula and scraping down sides of pan constantly, until mixture begins to thicken, about 10 minutes. (The mixture should have a gentle boil. Do not let eggs scramble. If mixture becomes too hot, remove pan from heat, while stirring constantly, until cooled down slightly. Then return to heat.) Remove from heat, and stir in toasted flaked coconut and vanilla. Transfer custard to a medium heat-proof bowl, and chill, stirring occasionally until completely cooled, about 1 hour.

Prepare the Chocolate Frosting: Beat powdered sugar, cocoa, and butter with an electric mixer on low speed until well blended, about 1 minute. Increase speed to medium, and beat until fluffy, 2 to 3 minutes. Scrape down sides of bowl, and beat in evaporated milk and vanilla extract on low speed until just incorporated, about 30 seconds. Increase speed to medium, and beat until light and fluffy, about 2 minutes. Transfer frosting to a piping bag fitted with a star attachment.

Assemble the Cupcakes: Pipe 1/4 cup chocolate frosting in a circle around tops of each cupcake, leaving an opening in center. Spoon 1 1/2 tablespoons coconut custard in center of each circle, and top with 1/2 tablespoon glazed pecans. Serve immediately. Cupcakes can be chilled without glazed pecans up to 24 hours. If chilled, remove cupcakes from refrigerator 30 minutes before topping with glazed pecans.