Preheat oven to 375°. Coat 12 standard 2½-inch muffin cups with cooking spray.
Put raisins in a small bowl and cover with hot water. Set aside.
Whisk whole-wheat flour, all-purpose flour, baking powder, salt and cinnamon in a large bowl.
Stir in bran.
Whisk egg, milk, apple butter, brown sugar (or Splenda), oil and molasses in a large bowl until blended.
Make a well in the dry ingredients and pour in the wet ingredients.
Drain the raisins; add them and the diced apple to the bowl.
Stir with as few deft strokes as possible until the batter is evenly moistened.
Scoop the batter into the prepared pan (the cups will be very full).
Bake the muffins until the tops spring back when touched lightly, 18 to 22 minutes.
Let cool in the pan for 5 minutes. Loosen the edges and turn the muffins out onto a wire rack to cool slightly before serving.