Preheat the oven to 350°F (175°C) and line two muffin pans with 16 liners.
Toast the shredded coconut: spread it on a rimmed baking pan and bake 5–8 minutes, stirring every 3–4 minutes, until lightly browned; watch closely to avoid burning. Remove and set aside.
Whisk dry cupcake ingredients: in a medium bowl, combine coconut flour, 1/2 teaspoon baking soda, and 1/4 teaspoon salt; set aside.
Mix wet cupcake ingredients: in a stand mixer fitted with the paddle or in a large bowl with a hand mixer, beat the 2/3 cup melted butter, 1 cup plus 2 tablespoons packed dark brown sugar, 8 eggs, 1/2 cup whole milk, and 4 teaspoons vanilla until well combined.
Combine batter: add the dry mixture to the wet and beat at medium speed until no lumps remain and the batter is smooth.
Fill liners about four-fifths full (just under 1/3 cup batter each) and bake 20 minutes, or until a toothpick inserted in the centers comes out clean. Cool in the pans 5 minutes, then transfer to a wire rack to cool completely.
Make the ganache: place 3/4 cup chopped chocolate in a small bowl. Heat 6 tablespoons cream in a small saucepan until hot and steamy (do not boil). Pour over the chocolate and stir until smooth. Let sit 5–10 minutes to thicken slightly.
Dip the tops of the cooled cupcakes into the ganache and return them to the wire rack. Chill briefly in the refrigerator to set the chocolate.
Make the caramel coconut topping: in a heavy-bottomed saucepan over medium heat, combine 3/4 cup packed dark brown sugar, 2/3 cup whipping cream, 7 tablespoons unsalted butter, 1 teaspoon vanilla, and 3/8 teaspoon salt. Stir until combined and no butter chunks remain, then simmer (do not stir) for about 8 minutes, adjusting heat as needed and tilting the pan to redistribute if necessary. Remove from heat.
Cool the caramel about 20 minutes until considerably thickened but still barely pourable, then stir in the toasted coconut.
Spoon just over 1 tablespoon of the caramel-coconut topping onto each ganache-dipped cupcake.
Use the remaining ganache to pipe or drizzle over the caramel topping using a piping bag or fork.