Preheat oven to 350 degrees. Line 24 cupcake molds with paper liners. Set aside.
In a large stand mixer bowl, add sugar, flour, cocoa powder, baking soda, baking powder, and salt on low until completely combined. In a separate medium bowl, whisk together eggs, egg yolk, sour cream, milk, and vanilla until completely combined.
With the mixer on low, slowly pour in canola oil into dry ingredients. Mix until combined but the dry ingredients will have large crumbs still. Add the rest of the wet ingredients and mix just until all lumps are removed and the batter is smooth. With the mixer still on low, pour in the hot brewed coffee. Mix until completely combined.
Using a cookie scoop, scoop batter into each prepared cupcake liner until 2/3 full. Place filled cupcake pans into prepared oven and bake until a tooth pick comes out clean when inserted in the center, about 15 mins. Remove from oven and let them cool in the pan for 5 minutes. Remove cupcakes from the pans and let cool on a rack completely before filling.
While the cupcakes cool, make the filling. Add cocoa powder and cornstarch to a large sauce pan and whisk together to remove lumps. Slowly whisk in the heavy cream together until combined. Add the milk, brown sugar, egg yolks, and salt and whisk until combined. Place over medium heat to warm up the mixture. Continue to whisk until the mixture starts to steam and thicken. Remove from heat and add the milk chocolate a little at a time until melted through. Finish with the vanilla extract.
Strain the pudding through a sieve to remove lumps. Cover with plastic wrap, making sure to touch the plastic to the pudding to prevent a film from developing. Refrigerate until cold, about 3 hours.
Cut a 1-inch circle in the center of each cooled cupcake and remove some of the filling underneath. Save the filling for later. Place 1 teaspoon of chocolate pudding in the center of each cupcake. Replace the cake on top of the pudding centers. You won't be able to replace the entire piece but just make sure the top is covered so you don't see too much of the pudding.
Make the fudge frosting by first whipping the butter in a stand mixer using a beater attachment. Whip for 1 minute. Add powdered sugar and cocoa powder. Mix on low until combined and then add the boiling water to make the texture smooth. Increase to medium high and whip for 3 minutes.
Transfer frosting to a pipping bag with a star tip. Squeeze a circle of frosting over the center of each cupcake. Sprinkle cupcake tops with any remaining pieces of cake that you saved from earlier.
Serve cupcakes immediately or place in refrigerator for up to 3 days.