Cupcakes: Preheat oven to 350F. Brush standard muffin tins with butter; dust with cake flour, tapping out excess. Whisk together cake flour, baking soda and salt.
With an electric mixer on medium-high speed, cream butter and sugar until pale and fluffy.
Add eggs one at a time, beating until each is incorporated, scraping down sides of bowl as needed.
Beat in vanilla. Reduce speed to low.
Add flour mixture in three batches, alternating with two additions of buttermilk, and beating until combined after each.
Beat in chocolate until combined.
Divide batter evenly among prepared cups, filling each three-quarters full. Bake rotating tins halfway through, until a cake tester inserted in the centers comes out clean, 20 minutes.
Transfer tins to wire racks to cool for 10 minutes. Run a small offset spatula or knife around edges to loosen; turn out cupcakes onto racks and let cool completely.
To finish, use a serrated knife, and a gentle sawing motion, to split cupcakes in half horizontally. Spread a heaping tablespoon of frosting on top of each bottom half; replace top halves and spread more frosting on top of each cupcake.
FROSTING: Combine egg yolks, evaporated milk, and brown sugar in a saucepan.
Add butter and cook over medium heat, stirring constantly, until thick, about 10 minutes. Pour through a fine sieve into a bowl.
Stir in vanilla, salt, coconut and pecans. Let cool completely.