Preheat oven to 375 degrees F. Lightly oil 18 muffin cups or coat with nonstick spray.
In a medium bowl, whisk together eggs, apple butter, oil and vanilla.
In a large bowl, stir together flours, sugar, cinnamon, baking powder, baking soda and salt.
Stir in the carrots, apples and raisins. Stir in apple butter mixture and mix until just moistened. Spoon the batter into the prepared muffin cups, filling them about ¾ full.
In a small bowl, combine walnuts and wheat germ; sprinkle over the muffin tops.
Bake for 20 minutes, or until tops are golden and spring back when lightly pressed.
Recipe by Dallas Duo Bakes at http://dallasduobakes.com/2016/01/morning-glory-muffins.html