Preheat oven to 375°F/190° C. Put the raisins in the small bowl and cover with hot water. Set aside for about 15 minutes.
In the large mixing bowl, whisk the whole-wheat flour, all-purpose flour, bran, baking powder, salt and cinnamon.
In the medium bowl, whisk the egg, milk, apple butter, brown sugar, oil, and molasses until blended. Make a well in the dry ingredients and pour in the wet ingredients. Drain the raisins and add them and the grated apple to the bowl. Stir just until combined, but don’t over mix. Divide the batter evenly in the prepared muffin pan. Each cup will be full.
Bake the muffins in the preheated oven until the tops spring back when touched lightly, about 18 to 22 minutes. Let cool in the pan for 5 minutes, then loosen the edges and turn the muffins out onto a wire rack to cool slightly before serving.