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.
To freeze: Place completely cooled muffins into gallon sized freezer zip bags in one layer, about 9 will fit in a bag. Using a straw, remove any excess air and zip the bag. Place in the freezer, it’s ok to stack the bags on top of each other, for up to 2 months (good luck getting them to last that long!).
Remove as many muffins as you need at a time and either thaw at room temperature or heat in the toaster oven or microwave. Frost with the sweetened cream cheese, if desired.
For the sweetened cream cheese: Place all the ingredients in a food processor and process until smooth. Alternatively, you can use a bowl and a hand mixer. Cream cheese will store for up to a week in the refrigerator. (I have not tested freezing it.).