Preheat oven to 350°.
Line cupcake pans with liners for 18 cupcakes. Use 2 for each if your liners are thin.
Add cake mix to a mixer bowl with 1/3 cup melted butter, 3 large eggs, coffee and 1/4 cup Kahlua.
Beat at low speed just until combined. Raise to medium speed and beat for 2 minutes.
Spoon into cupcake pans filling 3/4 full.
Bake 18-22 minutes or until a toothpick inserted comes out clean.
Remove from oven and cool in pan a few minutes. Move to a wire rack to cool completely.
Make the ganache: Add chocolate chips to a heat safe bowl. Heat heavy cream over medium heat until bubbly. Pour over chocolate chip and let it set for 5 minutes. Whisk together until smooth. If chocolate doesn't melt smooth, microwave in 15 second intervals until smooth.
Whisk in 1/4 cup Kahlua. Refrigerate while you make the frosting.
In a mixer bowl, add 3 sticks of softened butter, powdered sugar, cocoa powder, cream and Kahlua. Beat at low speed until it comes together. Scrape down the sides and raise to medium and beat 2 minutes. Add additional cream if frosting is too thick. Beat until smooth and fluffy.
Scoop heaping teaspoonfuls of the center of each cupcake. Set aside for another use or to snack on.
Fill indentions with ganache.
Fill a piping bag with frosting and pipe over filled cupcakes.
Serve immediately or cover and refrigerate until ready to serve.