Preheat oven to 400 degrees. Line 2 muffin tins with parchment liners.
In a large bowl, whisk together the 2 1/4 cups flour, 3/4 cup granulated sugar, 3/4 cup brown sugar, 1 tablespoon baking powder, and 1/2 teaspoon salt.
In a medium bowl, whisk together the 2 eggs, 2/3 cup vegetable oil, 1 cup buttermilk and 1 teaspoon vanilla.
Gently fold the buttermilk mixture into the dry ingredients until just combined.
In a small bowl, whisk together the 1/2 cup Dutch process cocoa powder, 2 teaspoons espresso powder and 1/2 cup boiling water until smooth and shiny. Add to the batter and fold in until no streak remain.
Fold in the 1 cup dark chocolate chunks. The batter will be slightly runny, like a cake batter. Fill muffins cups 2/3 - 3/4 full. Sprinkle additional chocolate chunks over the muffins, if desired.
Bake for 15-17 minutes, or until a tester inserted in the center comes out clean. Remove the muffins to wire racks to cool.
While muffins are baking, make the ganache filling. Heat the 2/3 cup heavy cream in a saucepan or a microwave safe bowl until bubbles just start to form around the edges. Add the 1 cup semi-sweet chocolate chips or chunks and let stand for 2 minutes.
Whisk the chocolate and cream together until thickened, smooth and shiny. Let the ganache sit at room temperature until firm enough to pipe--the consistency of buttercream frosting.
When the muffins are mostly cool, puncture a hole in the center using a round piping tip. Transfer the ganache to a piping back with a round tip. Pipe the ganache into the hole, allowing a bit of ganache to cover the tops of the muffins.