Preheat oven to 350 degrees F.
Sift together flour, baking soda, baking powder, cocoa, salt, and sugar.
In separate bowl, mix melted butter, eggs, and vanilla.
Alternate adding the flour mixture and 1 cup milk into the butter & egg mixture until well blended. Add chocolate chips.
Fill cupcake liners half full and bake for 15-17 minutes. Let cool.
Make instant pudding according to directions. Add 1 tsp coffee extract.
Fill pastry bag with pudding and place a filling tip on the end. Stick the filling tip into the center of each cupcake at a 90 degree angle and squeeze in the filling until you can see the top crust bulge.
Drop a bit of each color of food coloring into a bowl. Use a new paintbrush to "paint" the insides of the pastry bag or decorator with the food coloring.
After the inside is painted, add the frosting. Using a star tip, apply frosting in a swirling motion. Add sprinkles, and enjoy!