Heat oven to 350°F. Line two standard cupcake pans with 18 foil or paper liners.
Whisk flour, cocoa, baking powder, coffee, baking soda and salt in bowl.
In a large bowl, with an electric mixer, beat butter until smooth. Beat in light-brown sugar until fairly smooth and no lumps remain. Beat in eggs, one at a time. Add flour mixture alternately with milk, beginning and ending with flour. Fold in 1/2 cup of the mini chips.
Divide batter evenly among prepared cupcake liners, about 1/4 cup batter in each. Bake at 350°F for 25 to 27 minutes, or until toothpick inserted in centers comes clean. Remove from pans; cool on a rack.
In a small saucepan, combine sugar and water. Bring to a boil over high heat and cook 3 to 4 minutes, just until it reaches soft-ball stage (a small drop of sugar mixture dropped into ice-cold water will form a limp, sticky ball that flattens when removed from water), or 238°F on a candy thermometer. Meanwhile, beat egg in a medium-size bowl until light and frothy. Beating continuously, slowly add sugar syrup. Beat in butter, a piece at a time, until thick and smooth. Tint with food coloring. Transfer to a pastry bag fitted with a medium-size leaf tip. Pipe petals on cakes, starting at edge and working almost to center. Fill each center of cupcakes with 1/2 teaspoon mini chips.