Preheat the oven to 350 degrees F. Line two 12-cup muffin pans with cupcake liners. Place a shortbread cookie in the bottom of each liner (see note about trimming if needed). Set aside.
For the cupcake batter, in a small bowl or liquid measuring cup, combine the cocoa powder and hot water and whisk until smooth. In another medium bowl combine the flour, baking soda, baking powder, and salt, and whisk to blend.
In a medium saucepan set over medium heat or in a microwave-safe bowl, add the butter and sugar. Cook or microwave, stirring occasionally, until the mixture is smooth and the butter is completely melted.
Transfer the mixture to the bowl of an electric mixer or use a handheld electric mixer and beat on medium-low speed until the mixture is cool, about 4-5 minutes. Add the eggs one at a time, mixing well after each addition and scraping down the sides of the bowl as needed. Blend in the vanilla and then the cocoa mixture until smooth.
With the mixer on low speed, add 1/3 of the flour and mix to combine. Add 1/2 of the sour cream; mix. Add another 1/3 of the flour and mix again followed by the rest of the sour cream. End with the last 1/3 of the flour mixture and mix until combined.
Fill the muffin cups 1/2 to 2/3 full. Bake until a toothpick inserted in the center comes out clean, about 18-20 minutes.Transfer the cupcakes to a cooling rack and let cool completely.
To make the ganache, place the chopped chocolate in a medium heatproof bowl. Combine the caramel sauce and cream in a liquid measuring cup and microwave in 30 second intervals bringing to a simmer. Pour the warm caramel/cream mixture over the chocolate in the bowl and let sit for 1-2 minutes. Whisk the mixture together until the chocolate is fully melted and a shiny, smooth ganache has formed. Stir in the coconut extract. Let the ganache rest until thick and spreadable (without dripping excessively). Spread a layer of ganache on top of each cupcake. There should be a bit of ganache leftover to drizzle on the cupcakes at the very end.
To make the topping, place the caramels and milk in a large heatproof bowl. Microwave in 1-minute intervals, stirring often, until the mixture is melted and smooth. Take care as caramels can burn really easily of overheated in the microwave (says one who has learned from experience). Stir in the salt and the coconut extract. Fold in the toasted coconut.
Scoop a small mound of the coconut-caramel mixture (about 1½ tablespoons each) and using lightly wet hands, if needed for the stickiness, press the mixture into a round shape and gently indent the center or push a hole all the way through - just like the Girl Scout Samoa cookies.
When all the cupcakes have been topped, warm the extra ganache slightly (10-15 seconds in the microwave) until it can be drizzled across the tops of the cupcakes. Drizzle lightly with a fork over the cupcakes.
Cupcakes are best served at room temperature (they can be refrigerated for up to a day; let them come to room temperature before serving).
Shortbread Cookies: if using storebought shortbread cookies, you'll most likely need to trim them down with a serrated knife or a small round cutter to fit in the bottom of the cupcake liners.
Coconut: keep in mind that the coconut used in the topping is lightly toasted so plan ahead and lightly toast it in the oven or on the stovetop in a skillet to use in the recipe.
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