Preheat the oven to 350‚ and line 2 muffin tins with 15 parchment liners.
Make the cupcakes. In a medium bowl, combine the almond flour, coconut flour, cacao powder, baking soda and salt. Stir to combine. In a large bowl, combine the butter and coconut sugar and beat with a hand mixer until combined and smooth. Add in the eggs and vanilla and mix again. Mix in the yogurt and then the dry ingredients, mixing until fully combined. Then add in the bourbon, water, and maple syrup and stir until batter is well mixed. Divide evenly between the muffin liners and bake for 22-24 minutes, until a toothpick inserted in the center comes out clean. Let fully cool before frosting.
Make the pecans. Add the butter, vanilla and pecans to a small fry pan and toast over low heat for 5 minutes. While those are toasting, place sugar in a small bowl. Once the pecans are done, place in the bowl of sugar and toss to coat. Remove ¼ cup of the pecans for the topping.
Make the frosting. In a medium bowl, combine the butter and maple sugar. Beat with a hand mixer until smooth and fluffy in texture, about 2 minutes. Add in the pecans and sugar mixture and bourbon and beat again. Frost each cupcake and then top with remaining candied pecans
Store covered at room temperature for 2 days and then in the fridge up to 10 days.