Center a rack in the oven and preheat to 350 (F). Prepare four 6-inch round cake pans by spraying generously with cooking spray and lining the bottoms with parchment paper circles; spray the parchment paper with cooking spray.
In a small bowl, combine 2 cups granulated sugar with fresh zest from 1 medium orange. Use your fingers to incorporate the zest throughout the sugar, rubbing the zest into the sugar. This will help release oils from the zest that will infuse your sugar with more flavor. Set aside.
In the bowl of a freestanding electric mixer fitted with a paddle attachment, combine sugar (from the 2nd step), 2 1/4 cups all-purpose flour, 1/2 cup plus 3 tablespoons natural unsweetened cocoa powder, 3/4 teaspoon baking powder, 3/4 teaspoon baking soda and 3/4 teaspoon kosher salt. Beat on low speed for around 30 seconds to blend the ingredients together until fully combined.
In a large bowl, whisk together 1 cup melted unsalted butter, 3/4 cup buttermilk, 2 large eggs, 2 large egg yolks, 1 teaspoon pure vanilla extract, 1/2 teaspoon pure orange extract and 1 tablespoon red food coloring gel until just blended.
Add the liquid mixture (from the 4th step) to the flour mixture in 2 batches, beating on low speed until blended. Once the liquid mixture has been added, increase the mixer speed to high and beat until smooth, no more than 30 seconds. Reduce the mixer speed back to its lowest setting and slowly pour in 3/4 cup boiling coffee. Be careful not to overmix! Beat until the coffee has just been blended, and the mixture turns into a dark maroon, almost brown color. The batter will be thin.
Divide the batter equally among the prepared pans and bake in the preheated oven for 30 to 35 minutes, or until a skewer inserted into the center of each cake comes out clean and the tops of each cake bounce back when gently touched. Transfer the cakes to a wire rack to cool for 15 minutes, before turning them out to cool completely. Remove the parchment paper and prepare the frosting only when the cakes have completely cooled and you're ready to start frosting the cake.