Preheat the oven to 350°F. Set racks in the upper and lower thirds of the oven.
In the medium bowl, sift together sugar, flour, cocoa powder, baking powder, baking soda, and salt into a large bowl. In the bowl of the stand mixer, mix on low the whole milk, butter, whole egg, yolk, vanilla, and almond extract just until combined. Add the flour mixture to the egg mixture and mix on low speed until the dry ingredients are wet, then beat on high speed for 1 minute. Add the boiling water and mix on low speed just until combined. The batter will be very thin.
Pour the batter into the three prepared cake pans, dividing it evenly. Put pans in the oven, two on the lower rack and one on the upper rack and bake for 12 minutes. Switch the pans and rotate them 180°, then bake for another 10 to 12 minutes, until a toothpick comes out clean. Watch the cakes carefully so that they do not dry out.
Cool the cakes in the pans on a wire rack for 15 minutes. Run a thin knife around the edges of the cakes and then turn them out onto the wire rack. Carefully peel away the parchment and allow to cool completely.
Move top rack to the middle of the oven. Reduce oven temperature to 325°F.
Spread the coconut in the rimmed baking sheet. Bake until golden, 12 to 18 minutes, stirring occasionally. Remove pan from oven.
Increase oven temperature to 425°F.
Pour the condensed milk into the 9-inch deep-dish pie plate and cover tightly with foil. Put the pie plate in the roasting pan and fill with hot water until the water reaches halfway up the pie plate. Bake for about 45 minutes, then add more hot water to the pan as necessary. Bake until the milk mixture is thick and brown, about 45 minutes more. Remove pie plate from water bath. Stir in the coconut, pecans, vanilla, and salt. Cover with foil and keep warm.
(Make while the dulce de leche is baking.) Melt butter in the 3-quart saucepan. Turn off the heat and remove the pan. Stir in the corn syrup and chocolate until the chocolate is completely melted. Pour 1 cup of the ganache into the small bowl and chill for about 1 hour, until it is thick and spreadable. Keep the remaining ganache in the pan at room temperature.
Put 1 cake layer on the covered cake round and set it on a rack over a baking pan. Set a spatula in the cup of water. Drop half of the dulce de leche filling by spoonfuls evenly over the layer and gently spread with the wet spatula. Continue dipping the spatula in the water so that the filling spreads more easily. Add the next cake layer and top with the remaining dulce de leche filling, spreading the same way.
Add the final cake layer and spread the chilled ganache evenly over the top and around the side of the cake. Warm the room temperature ganache over low heat, stirring, until glossy and pourable, about 1 minute. Pour the ganache over the top of the cake, making sure that it flows evenly over and around the sides. You can gently shake the rack to help distribute the ganache. Chill the cake in the refrigerator for 1 hour, them serve at room temperature. Keep any leftovers in the refrigerator.
Total cook time includes the cake, dulce de leche, and the ganache.