Preheat the oven to 350°F. Line 24 standard muffin tins with double cupcake liners. Separate the egg yolks from the whites while cold, then let the whites sit at room temperature while you prepare the batter.

Melt the chopped chocolate in ½ cup boiling water, stirring until completely smooth. Set aside to cool slightly. Sift together the cake flour, salt, and baking soda in a medium bowl.

Cream butter and sugar in a large mixing bowl until light and fluffy, about 3 to 4 minutes. Add egg yolks one at a time, beating well after each addition, then mix in the melted chocolate and vanilla until fully incorporated.

Add the flour mixture alternately with the buttermilk, beginning and ending with flour, mixing just until smooth. Do not overmix.

In a clean bowl, beat the egg whites to stiff peaks. Gently fold them into the batter in two additions, folding just until no streaks remain. Fill the liners about ¾ full and bake for 20 to 30 minutes, checking at 15 minutes. A toothpick inserted into the center should come out with a few moist crumbs. Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.

While the cupcakes cool, make the frosting: combine evaporated milk, sugar, egg yolks, butter, and vanilla in a medium saucepan. Cook over medium heat, stirring constantly, until thickened and coating the back of a spoon, about 12 minutes. Transfer to a heatproof bowl, stir in coconut and pecans, and let cool until thick and spreadable.

Make the ganache: place finely chopped chocolate in a heatproof bowl. Heat cream until just boiling, pour over the chocolate, and let sit 1 to 2 minutes. Whisk gently until smooth, then add butter and whisk just until glossy. Let cool until thick enough to scoop.

Using a small paring knife, cut a shallow cone-shaped cavity from the center of each cooled cupcake. Fill each cavity with ganache, then spoon the coconut pecan frosting generously over the top.