Preheat the oven to 425°F. Spray a 12-count regular sized muffin pan with nonstick spray or use paper cupcake liners and still spray or grease the pan. Whisk the flour, baking soda, cinnamon, nutmeg and salt in a large bowl. In a medium bowl, whisk the eggs, brown sugar, honey, oil, applesauce, orange zest, orange juice and vanilla together until combined. Whisk in the shredded carrots and grated apple. Pour the wet ingredients into the dry ingredients, stir a few times with a wooden spoon or rubber spatula, then add the pecans and cherries. Using the wooden spoon or spatula, fold everything together until just combined and all the flour is mixed in.