Preheat oven to 325 degrees. Line a standard 12 cup muffin pan with paper liners.
Make the frosting by bringing the coconut milk just to a boil in a saucepan. Turn off the heat, stir in 1 tablespoon of vanilla extract and 1 ¼ cup of the chocolate chips. Let sit for 5 minutes then stir well until the mixture is smooth and glossy. Pour into a medium mixing bowl and refrigerate until cold, at least half an hour.
In a mixing bowl, whisk together the almond flour, baking powder and salt. Put the egg yolks in one mixing bowl and the egg whites in another. Beat the egg whites on high speed until stiff peaks form. Add the remaining tablespoon of vanilla to the yolks along with the oil, agave and almond extract. Beat on high speed until the mixture becomes thicker and lighter in color, about 2 minutes. Take a scoop of the beaten egg whites and stir into the yolk mixture. Fold the remaining whites into the yolks. Add the flour mixture and fold in until fully combined. Add the remaining ½ cup of chocolate chips and the chopped cherries and mix. Divide the batter among the prepared muffin cups and bake for 30 minutes or until the cupcakes are browned, feel springy to the touch and a tooth pick inserted into the center comes out clean. Let cool in the pan for 15 minutes then remove to a wire rack to finish cooling.
When the frosting is cold, whip it on high speed with a hand held mixer until fluffy. Frost the cooled cupcakes and garnish with a maraschino cherry and a couple slices of almonds.