Preheat oven to 350°.
To prepare cupcakes, place 6 tablespoons butter and chocolate in a large microwave-safe bowl; microwave at high 1 minute, stirring after 30 seconds. Stir until chocolate melts. Stir in granulated sugar, water, and 2 teaspoons vanilla. Add egg substitute, stirring mixture with a whisk.
Lightly spoon flour into dry measuring cups; level with a knife. Combine flour, baking powder, baking soda, and salt, stirring with a whisk. Add flour mixture to chocolate mixture, stirring with a whisk until smooth. Place 18 paper muffin cup liners in muffin cups; spoon batter evenly into lined muffin cups. Bake at 350° for 18 minutes or until a wooden pick inserted in center of a cupcake comes out clean. Cool on a wire rack.
To prepare icing, melt 1/4 cup butter in a medium saucepan over medium heat. Add brown sugar; cook 3 minutes, stirring constantly with a whisk. Add milk, and cook 3 minutes, stirring constantly. Remove from heat; stir in 2 teaspoons vanilla. Gradually add powdered sugar, stirring with a whisk until smooth. Working quickly, spread each cupcake with about 1 1/2 tablespoons frosting; sprinkle cupcakes evenly with pecans and coconut.