Preheat oven to 375 degrees. Add brown baking cups* into a jumbo six cup muffin tin.
Add the milk, water and coffee into a saucepan and simmer. Add the cocoa powder, chocolate chunks and butter. Mix until melted, transfer into a bowl and let cool.
In a separate bowl, add the flour, baking powder and salt and mix.
Into the cooled chocolate add the sugars, oil, eggs and vanilla and mix together. Using a spatula add 1/3rd of the flour and blend in. Then fold in the remaining flour until just incorporated and you no longer see any flour. Fold in the remaining 1/3 cup of chocolate chunks.
Bake for 24 minutes until the top of the muffin bounces back when lightly touched. The chocolate chunks will have melted so you aren't going to be able to do a toothpick test. Let the muffis completely cool on a cooling rack.
For the Filling
In a double boiler heat the cream, and then add the chocolate chunks and stir until fully melted. Finish with the pinch of salt.
Let cool.
Final Assembly
Make a divot in the middle of the muffin and spoon in the ganache filling.
Notes
*you can make your own muffin cups with parchment paper:To start, cut a piece of parchment paper in 6-inch squares. Lay the paper atop the muffin pan and roughly estimate the inner corners of the cup (Cut slits roughly the same length as your pan is high into the parchment paper, from edge to center, where you estimate each of the four corners to be. Don't cut too far in — the slits should not touch, as that would cut through the parchment entirely.Then, when you push the parchment down into each cup of the pan, the edges magically fold in on each other, creating a perfect parchment liner.If this is all too fussy for you, you can skip the cutting step and use a small can to push the paper down into the mould. Smooth any creases created to ensure the batter doesn't get stuck in them.