Heat oven to 375. Spray 24 muffin cups w/ cooking spray or use muffin liners. Sift together flours, 1 tsp cinnamon, nutmeg, ginger, cloves, allspice, baking powder and baking soda into a lg bowl.
In another lg bowl, Beat 1/2 cup butter, sugar and brown sugar until fluffy. Add eggs, one at a time, beating after adding each one. Add milk and pumpkin puree. Beat in flour mix until just combined. Stir in cranberries. Spoon batter into muffin cups, about 1/4 cup each muffin cup.
Bake 25 mins, or until a toothpick inserted in center comes out clean. In medium bowl, beat cream cheese and butter until smooth. Beat in powdered sugar, slowly. add vanill and cinnamon. Beat until fluffy. Frost cooled cupcakes. I always place a candy corn on top of each muffin for a halloween treat.