Preheat oven to 350°F.
Line about 18 2.5" muffin cups with cupcake liners.
In a bowl, combine flours, sugars, cocoa powder, baking soda, and salt.
In another bowl, combine milk, applesauce, oil, molasses, balsamic vinegar, and vanilla extract.
Mix wet mixture into dries. Stir just until moistened, batter should be lumpy.
Stir in half of the chocolate pieces.
Spoon batter into prepared muffin cups, filling each cavity just over half way. Divide remaining chocolate between the tops of the cupcakes.
Bake for 15 minutes.