Preheat oven to 375°.
Lightly spoon flours into dry measuring cups; level with a knife. Combine flours and the next 8 ingredients (all-purpose flour through salt) in a large bowl, stirring well with a whisk. Stir in carrot, apple, and raisins.
Combine milk, oil, vanilla, egg whites, and orange in a blender or food processor; process until smooth. Make a well in center of flour mixture; add milk mixture; stir just until moist.
Spoon 3 tablespoons batter into each of 28 muffin cups coated with cooking spray. Bake in batches at 375° for 20 minutes or until muffins are browned and spring back when touched lightly in center. Remove the muffins from pans immediately, and place on a wire rack.