Preheat oven to 350° F. Grease or line 18 muffin cups with paper liners.
In a large bowl, combine flours, sugar, cinnamon, nutmeg, baking soda and kosher salt. Whisk the dry ingredients until thoroughly combined.
In another bowl, combine the eggs, applesauce, vegetable oil and vanilla. Stir in carrots, zucchini, apple, pineapple, coconut and pecans.
Add wet ingredients to dry ingredients and mix until thoroughly combined, but do not overmix.
Divide batter evenly between the prepared muffin cups. Bake in preheated oven for 20-24 minutes, or until a toothpick comes out clean.
Allow muffins to cool in the pan for about 5 minutes before removing to a wire rack.
Notes
For sweeter muffins, use sweetened applesauce and/or sweetened coconut. For less-sweet muffins, use unsweetened applesauce and/or unsweetened coconut.If you do not have whole wheat flour, feel free to substitute an equal amount of all-purpose flour.These muffins are best served the same day; however, they will keep in an airtight container for up to 2 days, or freeze them for up to a month for longer-term storage.