Preheat oven to 200 C / 400 F. Line a 12-cup muffin tin with cupcake liners. Line another 12 cup muffin tin with 10 cupcake liners. Set aside.
Place flour, brown sugar, granulated (caster) sugar, cocoa powder, baking soda, baking powder and salt in a large bowl. Whisk to combine. Set aside.
Make a well in the center in the middle and add eggs, sour cream and oil. Fold gently until just combined. Avoid overmixing. The batter will be thick and sticky.
Pour in hot coffee. Fold in gently to make smooth batter.
Add ½ cup chocolate chunks. Fold in gently.
Spoon ¼ cup batter into each liner.
Top with remaining chocolate chunks.
Transfer muffin tins to oven. Reduce temperature to 180 C / 350 F.
Bake for 20-22 minutes or until a skewer inserted into the centre comes out clean.
Cool muffins in the pan for about 10 minutes, and then transfer to a wire rack to cool completely.
To make chocolate ganache, pour warm cream over chocolate and stir until chocolate melts completely. The ganache will be thick, smooth and shiny. Place ganache in piping bag fitted with piping nozzle. Pipe ganache into cooled muffins.
Store leftover muffins (without ganache) in an airtight container in the refrigerator for about 3-4 days.