For the cupcakes, preheat oven to 350°F. Line a 24-cup cupcake tin with liners (preferably something green). Combine Guinness and butter in a heavy saucepan over medium heat, and simmer until melted. Add the cocoa powder and whisk until the mixture is smooth. Cool slightly.
Mix together your dry ingredients combining the flour, sugar, baking soda and salt in a large bowl. Using an electric mixer, beat the eggs and sour cream on medium speed until combined. Add the cooled Guinness-chocolate mixture to the egg mix and beat until just combined. Reduce the speed to low, add the flour mixture part by part and beat briefly. Using a rubber spatula, fold the batter until completely combined. Divide the batter among the cupcake liners, filling each cup approximately ¾ full. Place the cupcake pan into the oven and bake about 17 minutes, or until a toothpick comes out clean. Cool the cupcakes on a cooling rack.
For the whiskey ganache filling, chop the bittersweet chocolate and transfer it to a heat safe bowl. Heat the cream in a small saucepan until simmering and pour it over the chocolate. Let it sit for a minute or two. Use a spatula and mix together until smooth. Add butter and whiskey and mix together. Let the ganache cool until thick but be sure to time it so that it is still soft enough to be piped. Use a 1″ scoop (melon baller works great) to cut the centers out of the cooled cupcakes, scooping the centers out about ¾ of the way down. Transfer the ganache to a piping bag with a wide tip and fill the holes in each of the cupcakes to the top.
For the frosting, use an electric mixer and whip the room temperature butter and softened cream cheese on medium-high speed for about 5 minutes until well mixed. Reduce the speed to medium-low and feed in the powdered sugar gradually until it is mixed. Add ICL , increase the speed to medium-high and whip for another 2 to 3 minutes, until it is light and fluffy. Use a decorating tip or spread the frosting atop of the cupcakes.