Preheat oven to 350°.
Lightly spoon flours into dry measuring cups; level with a knife. Combine flours, granulated sugar, and next 7 ingredients (through nutmeg) in a large bowl, stirring well with a whisk.
Spread zucchini onto several layers of heavy-duty paper towels; cover with additional paper towels. Press down firmly to remove excess liquid.
Combine yogurt, egg substitute, oil, and vanilla in a medium bowl, stirring well with a whisk. Stir in zucchini.
Add zucchini mixture and 1/4 cup pecans to flour mixture, stirring until well combined. Pour batter into a 9 x 5-inch loaf pan coated with cooking spray. Sprinkle batter with 3 tablespoons pecans. Bake at 350° for 1 hour or until a wooden pick inserted in center comes out clean. Cool in pan 10 minutes on a wire rack. Remove bread from pan; place on wire rack.