Make the cupcakes: Position a rack in the middle of the oven and preheat to 325 degrees F. Line two 12-cup muffin pans with paper liners. Whisk the whole eggs and egg whites in a large bowl. Whisk in the cream of coconut and the coconut and vanilla extracts until smooth.
Whisk the flour, sugar, baking powder and salt in a large bowl. Beat in the butter, one piece at a time, with a mixer on low speed until the mixture resembles coarse meal, 3 to 4 minutes. Add half of the egg mixture, increase the speed to medium-high and beat until fluffy, about 1 minute. Beat in the remaining egg mixture until combined, scraping down the bowl as needed.
Divide the batter among the prepared cups, filling each about halfway. Bake until a toothpick inserted into a cupcake comes out clean, 18 to 22 minutes. Let cool in the pans 10 minutes; transfer to racks to cool completely.
Make the topping: Combine the milk, coconut, confectioners' sugar, vanilla and salt in a medium saucepan. Bring to a simmer over medium-high heat and cook until the milk is absorbed and the mixture thickens, stirring occasionally, about 15 minutes. Cool completely.
Make the glaze: Put the chocolate, corn syrup, butter and 3 tablespoons hot water in a microwave-safe bowl, cover with plastic wrap and microwave on 50 percent power until the chocolate melts, about 2 minutes. Whisk to combine. Keep warm.
Top each cupcake with a heaping tablespoonful of the coconut mixture, pressing gently until compact. Spoon 1 teaspoon glaze on top and garnish with 2 almonds. Refrigerate until the glaze sets, about 20 minutes.