Bake 24 cupcakes according to the box instructions. Let cool completely.
In the bowl of a stand mixer fitted with the paddle attachment, add 1 cup of the shredded coconut. Turn the mixer on low, add 8 drops of yellow food coloring and mix until the coconut is a uniform bright yellow. Transfer to a bowl. Add another cup of the coconut to the bowl and turn the mixer on low. Add 6 drops of yellow food coloring and 4 drops of red food coloring and mix until the coconut is a uniform reddish orange (add a few more drops of each if the color is not vibrate enough). Transfer the coconut to a separate bowl. Wash and dry out the standing mixer bowl and add the remaining 1 cup coconut. Turn the mixer on low and add 6 to 8 drops of blue food coloring. Mix until the coconut is a uniform bright blue. Transfer to a third bowl.
In a medium bowl, mix together the chocolate candies, fruit candies and nonpareils. Set aside.
Using a 1/2-inch round cutter, cut out a well in each cupcake (reserve the cut-out top pieces of each cupcake). Use a small spoon to scoop out the wells, being careful not to go all the way through the bottom of the cupcakes. Fill each cupcake well about two-thirds full with the mixed candy, about a heaping tablespoon. Cover the holes with the reserved cut-out tops.
Frost the cupcakes with the vanilla frosting. Press some of the blue coconut onto the outer third of the top of each cupcake to form a stripe, then press some of the yellow coconut in the center third and finally the orange coconut in the final third. You should have 3 equal stripes on the top of each cupcake.