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Sift the flour, baking powder, baking soda and salt into a medium bowl. Set the bowl aside. In the bowl of an electric stand mixer with a paddle attachment, cream the brown sugar and butter together, about 5 minutes. Scrape down the sides of the bowl. Then add the vanilla and eggs, one at a time, scraping down the sides of the bowl after each addition. Turn the mixer to the lowest speed, and add the flour mixture and the milk, alternating between the two, beginning and ending with the flour. Take the bowl off the stand mixer and stir in the chocolate chips by hand until thoroughly combined.
Fill 36 mini cupcake liners three-quarters full with batter and bake until baked through, about 15 minutes (or fill 24 regular cupcake liners three-quarters full with batter and bake for 24 minutes). Cool the cupcakes completely.
To assemble: Using an apple corer, core each cupcake and throw away the pieces removed. Roll the Edible Cookie Dough into a rod shape and fill the center of each cupcake. While the Chocolate Fudge is still warm, spread on top of each cupcake. Once the chocolate fudge has completely cooled, frost each cupcake with the Vanilla Buttercream. Use 2 Chocolate Chip Cookies and spread one side with the chocolate fudge and the other with the vanilla buttercream. Sandwich the cookies together. Place the cookie sandwich on top of each cupcake.
Consumption of raw or undercooked flour may increase the risk of foodborne illness.