Preheat oven to 350 degrees F. Butter and line bottoms of three 6-inch cake pans with parchment paper rounds.
Add the chopped bittersweet chocolate and espresso powder to a small bowl. Pour boiling water over chocolate. Let set for 5 minutes. Stir to ensure chocolate has melted. Set aside to cool.
Sift the all-purpose flour, unsweetened cocoa powder, black cocoa powder, baking soda, baking powder, and fine sea salt into a large mixing bowl. Set aside.
Add the unsalted butter to stand mixer bowl. Using paddle attachment beat butter on medium speed 2 minutes. Add the light brown sugar and granulated sugar to the stand mixer bowl. Beat on medium speed 2 minutes, or until light and fluffy.
Add the eggs and yolks to the stand mixer bowl, one at a time. Beat on low speed after each addition, for about 30 seconds or until fully incorporated.
Add half the flour mixture to the stand mixer and beat on low just until incorporated. With the motor running, stream in the whole milk. Stop the mixer and add the remaining flour mixture. Beat on low just until incorporated.
Add the chocolate espresso mixture and beat on low until incorporated.
Divide the cake batter evenly between the three prepared cake pans. Smooth top with small offset spatula. Bake cake layers in preheated oven to 33 minutes, or until center of cakes are firm and a toothpick inserted in the center of each cake comes out clean.
Remove cake pans from oven and cool on wire racks. Cool cakes completely before removing them from their pans and frosting. Remove parchment rounds from the bottom of cake layers. Level cake layers with a long serrated knife. Reserve the cut off portions, as we need them to coat the cake.