Preheat the oven to 425 degrees F. Lightly coat the top of a standard 12-cup muffin pan with nonstick spray and line with standard cupcake liners.
Whisk the whole wheat flour, all-purpose flour, baking powder, salt, cinnamon, ginger and baking soda in a large bowl to combine. Add the carrot, apple, coconut, pecans, raisins and orange zest and toss to coat.
Whisk the dark brown sugar, eggs, yogurt and oil in a medium bowl until combined and creamy, about 30 seconds. Gently fold the egg mixture into the dry ingredients just to combine (be careful not to overmix, it's ok if bits of flour are showing).
Divide the batter evenly among the muffin cups. Top each muffin with 1/2 teaspoon of the raw sugar.
Bake the muffins, rotating the pan halfway through, until a tester inserted into the center comes out clean, 28 to 33 minutes. Transfer the pan to a wire rack and let the muffins cool in the pan 5 minutes. Remove from the pan and place onto the rack to cool completely.