Preheat the oven to 350 degrees F. Spray a 6-cup muffin tin with nonstick cooking spray, then sprinkle lightly with flour.
In a large bowl, combine the all-purpose flour, whole-wheat flour, sugar, raisins, wheat germ, baking powder, baking soda, and salt. In a medium bowl, whisk the pumpkin puree, egg, orange juice, pumpkin pie spice, and vanilla. Add to the flour mixture; stir until just combined. (Do not over mix).
Spoon the batter into the cups, filling each about 2/3 full; sprinkle with the walnuts. Bake until a toothpick inserted in a muffin comes out clean, 25-30 minutes. Cool in the pan on a rack 10 minutes; remove and serve warm.