Preheat oven to 400 degrees. Coat a standard (12-cup) muffin tin with cooking spray. Whisk together flours, pecans, wheat germ, brown sugar, baking powder, baking soda, cinnamon, and salt.
Stir together carrots, zucchini, yogurt, egg yolks, molasses, and orange zest in a large bowl. Fold flour mixture into carrot mixture until just combined. With a whisk or a mixer fitted with the whisk attachment, beat egg whites until shiny, stiff peaks form. Gently fold egg whites into the carrot mixture.
Spoon batter into prepared tin, filling to the brims. Bake until a toothpick inserted into center of 1 comes out clean, about 25 minutes. Let cool completely in pan on a wire rack. (Muffins can be stored in an airtight container at room temperature for up to 3 days.)