Preheat oven to 350 degrees F. Line 36 muffin cups with baking liners.
Grate the carrots (I use a box grater and use the second largest sized hole). Set aside.
In a medium sized bowl, combine the carrots, flours, flax, baking powder and soda, cinnamon and allspice. Stir to mix well. Set aside.
Combine the brown sugar and butter in a large bowl. Beat using a stand mixer or a hand mixer until smooth. Add the eggs and beat until incorporated. Stir in the yogurt, pumpkin, orange juice, and vanilla.
Add the flour mixture to the sugar/butter/egg mixture. Stir with a wooden spoon until well mixed, but do not over beat.
Add a scant 1/4 cup of batter to each muffin cup, making about 36 muffins in all. Bake at muffins at 350 degrees for 14-16 minutes, or until cooked through when tested with a toothpick. Remove muffins from the pan and cool on a wire rack completely.