Sift the flour, cocoa powder, baking powder, and baking soda right into the wet mixture. Stir with a whisk or wooden spoon just until the flour mostly disappears. Don't overmix here!
Add the hot coffee to the bowl and stir gently until the batter is smooth. The batter will be very thin, which is exactly how it should look.
Fill each cupcake liner about ⅔ full. Bake at 180°C (350°F) for roughly 20 minutes, or until a toothpick inserted into the middle comes out clean.
Let them cool in the pan for 10 minutes, then move them to a wire rack to cool completely.
Make the cherry filling
Put the pitted cherries, lemon juice, and sugar into a medium saucepan over medium heat. Stir occasionally until the cherries soften and start releasing their juices.
In a small cup, mix the cornstarch with a tablespoon of cold water until smooth.
Pour this slurry into the simmering cherries while stirring constantly. Cook for another 2–3 minutes until the sauce bubbles and thickens up.
Remove the pan from the heat and stir in the Kirsch. Let the filling cool completely before using (it will get thicker as it sits).
Make the whipped cream
Add the cold heavy cream, instant pudding powder, vanilla extract, and powdered sugar into a large bowl. Beat with an electric hand mixer on high speed for a few minutes until you get thick, stiff peaks.
Assembly
Use a cupcake corer or a knife to cut a small well out of the center of each cooled cupcake (don't go all the way to the bottom!). Spoon a generous amount of the cooled cherry filling into the centers.
Put the whipped cream into a piping bag fitted with a star tip and pipe a big swirl onto each cupcake.
Drizzle some leftover cherry juice over the top, add some chocolate shavings if you like, and finish with a fresh cherry.
Notes
Don't Skip the Coffee: The heat from the coffee brings out the absolute best flavor in the cocoa powder. The cupcakes will not taste like coffee at all.
Let Everything Cool Completely: If the cupcakes or the cherry filling are even slightly warm, the whipped cream will instantly melt into a watery mess.
Don't Overcore the Cupcakes: Only cut about halfway down into the cupcake. If you cut all the way to the bottom paper liner, the juicy filling will leak out and make a mess.
Stop Whipping in Time: Keep a close eye on the whipped cream. The second it holds a sharp, stiff shape, stop mixing. Over-whipping will turn the cream grainy.