Preheat oven to 425 degrees. Line two 12-count muffin pans with cupcake liners, just enough for 16 muffins, and lightly spray the bottom of each liner with cooking spray.
In a large bowl, whisk together whole wheat flour, baking soda, cinnamon, ginger, salt, and chopped pecans; set aside.
In another bowl, stir together the eggs, brown sugar, honey, oil, applesauce, lemon zest, and the drained pineapple juice. Make a well in the dry ingredients, then pour in the wet ingredients and stir gently. Fold in the pineapple, carrots, coconut, and Craisins (be sure to drain off the water) just until combined.
Evenly divide the batter between the liners, filling them to the top. Bake at 425 degrees for 5 minutes. Without opening the oven door, reduce the oven temperature to 350 degrees and continue baking for another 18-20 minutes or until a toothpick inserted in the center comes out clean.
Remove from oven and allow muffins to cool for 10 minutes in the muffin tin before transferring to a wire rack. Drizzle warm muffins with honey cream cheese glaze and sprinkle more coconut and chopped pecans on top—gently pressing into the glaze—if desired.
Honey Cream Cheese Glaze
In a small bowl, whisk together all the glaze ingredients until smooth. Drizzle over warm muffins. If you prefer to completely cover the muffin tops, double the glaze recipe.
This muffin recipe makes 16 muffins, so you'll need to use TWO regular size muffin pans. Place 16 paper liners in the cups in the muffin pans, then after filling them with batter add a couple tablespoons of water to the empty cups in the pan. This will ensure uniform baking.