Preheat oven to 425°F (218°C)7. Spray a 12-count muffin pan with nonstick spray or use greased/sprayed cupcake liners. This recipe makes 16 muffins, so prepare a second muffin pan in the same manner. In a large bowl, whisk the flour, baking soda, cinnamon, ginger, salt, flax, and pecans together until combined. Set aside. In a medium bowl, whisk the eggs, brown sugar, honey, oil, applesauce, orange zest, orange juice, and vanilla together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, then add the raisins, carrots, and apple. Fold everything together gently just until combined and no flour pockets remain. Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425 then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 18 minutes or until a toothpick inserted in the center comes out clean. The total times these muffins take in the oven is about 23-24 minutes, give or take. Allow the muffins to cool for 10 minutes in the muffin sheet, then transfer to a wire rack to cool until ready to eat. Make ahead tip: Muffins stay soft, fresh, and moist at room temperature for up to 5 days. Muffins freeze well for up to 2 months. Thaw overnight in the refrigerator and heat up (if desired) before enjoying.