Preheat oven to 350. Line 3 cupcake pans with liners. If using the foil liners, remove the paper insert so you're just using the foil part. Beat together all cupcake ingredients (besides chocolate chips) until smooth. Beat in chocolate chips on low until well incorporated. Batter will be thick.
Divide batter evenly between the 36 cups. (You're dividing the batter between 36 instead of 24 cups because you don't want domed cupcakes for these) Bake for 18-20 minutes until a toothpick inserted in the center comes out clean. You'll have to bake them in 2 batches to cook them all. Cool completely.
Using a knife (or a cupcake corer, if you have one) cut a circle into the top of the cupcake, removing part of the center, but not to the bottom of the cupcake. Save removed sections.
FOR THE CREME FILLING: In a large bowl, beat together the marshmallow creme and shortening until smooth. Add in powdered sugar, 1/3 C at a time, beating after each addition. Add in vanilla and salt and beat again. Add milk, a tablespoon at a time, beating after each addition, until the filling is smooth and fluffy.
Using a piping bag, or a ziploc bag with a corner clipped, pipe the filling into the centers of the cupcakes. Replace removed cupcake sections on top of the creme, pressing gently to flatten. (You may have to remove a bit from the bottom of the saved sections to fit on top of the creme)
FOR THE GANACHE: Place chocolate chips in a large glass bowl. Heat heavy cream on the stove over medium low heat until it just starts to boil, whisking occasionally to prevent scorching. Remove from heat and add in butter, whisking until melted. Pour hot cream over chocolate chips in the bowl. Whisk continually as chocolate is melting. It will go from white, to medium brown, then to dark shiny brown when all the chocolate is melted. It will be very runny. Put in the fridge for about 30 minutes, whisking occasionally, until it thickens up slightly.
Spoon over each cupcake. Let cool for about an hour before piping on decoration.
FOR DECORATION: Simply stir up frosting in jar, spoon frosting into a piping bag or ziploc bag, and pipe desired design on top of the cupcakes.