Preheat oven to 375°F. Lightly grease 2 baking sheets.
In a large bowl, combine all-purpose flour, whole wheat flour, baking powder, and baking soda. Mix in ginger, allspice, cinnamon, cloves, and salt. Set aside.
In another large bowl, cream butter until fluffy. Mix in applesauce, and slowly stir in 2¼ cups sugar until well blended. Mix in the eggs and pumpkin. Gradually mix flour mixture into the applesauce mixture. Stir in pecans.
Heap tablespoonfuls of mixture onto cookie sheets, leaving 2 inches between scones. Flatten scones with the back of the spoon.
In a small bowl, stir together 3 tablespoons of sugar and cinnamon, and sprinkle on top of scones.
Bake in preheated oven until golden brown, about 12 to 14 minutes.