Put 2 racks in the center of the oven, and preheat the oven to 350°F. Add liners to cupcake baking pan, sprinkle half the oats inside, and set aside.
In a medium bowl, sift together whole-wheat flour, protein powder, baking soda, cinnamon, ginger, and salt. Set aside.
In a large bowl, use an electric mixer on medium speed to combine brown sugar and oil. Beat in the yogurt and applesauce until fully combined. Mixture will be gritty and thin. Add the eggs one at a time, beating well after each addition. Mix in the vanilla.
With a spatula, manually stir the dry ingredients into the wet ingredients until just combined. All flour pockets should be gone, but do not overmix. Fold in the finely shredded carrots, shredded coconut, raisins, and walnuts. Divide batter among prepared cupcake pans. Sprinkle the remaining oats on top.
Bake for 20–23 minutes, or until a toothpick inserted in the center comes out clean or with a few crumbs.