Assumption: Preheat oven to 350°F (175°C). Line a 12-cup muffin pan with cupcake liners.
Mix the HOT COFFEE ingredients: dissolve coffee granules (if using) in hot water; set aside to cool slightly.
In a bowl, whisk DRY ingredients together (flour, cocoa powder, baking powder, baking soda, salt).
In a second bowl, whisk WET ingredients together (brown sugar, milk, oil, vanilla, vinegar, eggs) until smooth.
Add DRY to WET and whisk just until combined. Pour in the HOT COFFEE mix and stir until smooth.
Divide batter into liners, filling about 2/3 full. Bake 15–18 minutes (assumption), until a toothpick comes out with a few moist crumbs. Cool completely.
Make ganache: heat heavy cream until steaming. Pour over chocolate. Rest 2 minutes, then stir until smooth. Cool until thick enough to pipe/spread (assumption: 20–45 minutes).
Make filling: beat softened cream cheese until smooth. Add cold heavy cream and whip to medium-stiff peaks.
Core cupcakes and pipe filling into the center. Replace the cake “cap” if desired.
Frost cupcakes with thickened ganache. Let set at room temp or chill briefly to firm.