Preheat oven to 350 degrees. Line 12 standard muffin cups with paper liners.
In a small mixing bowl, whisk together the coconut flour, salt, and baking soda until the coconut flour is no longer lumpy.
In the bowl of an electric mixer, preferably fitted with a whisk attachment, beat the coconut oil and agave for 2 minutes. Add the eggs, one at a time, beating well after each addition. Add the extracts and beat well to combine. Add half of the flour mixture, then the coconut milk and finally the rest of the flour mixture. Beat until combined and not lumpy. With a spatula scrape the bottom and sides of the mixing bowl to ensure all the ingredients are properly combined. Fold in the coconut flakes. Divide the mixture between the prepared muffin cups and bake for 20 -25 minutes or until the cupcakes are golden brown and a toothpick inserted into the center comes out clean. Let cool in the pan for 10 minutes then remove to a wire rack to finish cooling. While the cupcakes are cooling, make the frosting.
In the bowl of an electric mixer, preferably fitted with a whisk attachment, beat the coconut oil with the extracts to combine. Add the powdered sugar, 1 cup at a time and blend after each addition. The mixture may look clumpy, this is ok. Add the coconut milk, 1 tablespoon at a time until the frosting reaches desired consistency – you want it similar to butter cream frosting. Continue to beat for 2 minutes.
Frost the cupcakes generously and top with the coconut chips or flakes. It is best to keep the cupcakes in the fridge if not serving immediately but take them out about 10 minutes before serving to take the chill off for best results.