Make the cupcakes: Preheat oven to 350°F. Line 24 cupcake cups with liners. Bring the Guinness and butter to simmer in heavy large saucepan over medium heat. Add cocoa powder and whisk until mixture is smooth. Cool slightly.
Whisk flour, sugar, baking soda, and salt in large bowl to blend.
In the bowl of an electric stand mixer fitted with the paddle attachment, beat eggs and sour cream. Add stout-chocolate mixture to egg mixture and beat just to combine. Add flour mixture and beat briefly on slow speed. Using rubber spatula, fold batter until completely combined. Divide batter among cupcake liners, filling them 2/3 to 3/4 of the way. Bake cake until tester inserted into center comes out clean, rotating them once front to back if your oven bakes unevenly, about 17 to 19 minutes. Cool cupcakes completely.
Make the filling: Chop the chocolate and transfer it to a heatproof bowl. Heat the cream until simmering and pour it over the chocolate. Let it sit for one minute and then stir until smooth. (If this has not sufficiently melted the chocolate, you can return it to a double-boiler to gently melt what remains. 20 seconds in the microwave, watching carefully, will also work.) Add the butter and whiskey and stir until combined.
Fill the cupcakes: Let the ganache cool until thick but still soft enough to be piped (the fridge will speed this along but you must stir it every 10 minutes). Meanwhile, using a 1-inch round cookie cutter, paring knife, or melon baller (my personal choice), cut the centers out of the cooled cupcakes. You want to go most of the way down the cupcake but not cut through the bottom — aim for 2/3 of the way. Put the ganache into a piping bag with a wide tip and fill the holes in each cupcake to the top.
Make the frosting: Whip the butter in the bowl of an electric mixer for several minutes until fluffy. Add the powdered sugar a little at a time, until fluffy and thick. Drizzle in the Baileys and whip it until combined. If this has made the frosting too thin (it shouldn’t, but just in case) beat in another spoonful or two of powdered sugar.
Frost the cupcakes as desired.