Preheat oven to 325 degrees. Line a muffin tin with muffin liners or spray with cooking spray. Set aside.
Whisk together the whole wheat pastry flour, pumpkin pie spice, salt, baking powder, and baking soda.
In a separate bowl combine the pumpkin, unsweetened applesauce, and honey. Whisk in the milk and vanilla and mix until smooth.
Add the dry ingredients to the wet and stir until combined. There may be a few small lumps left in the batter, but do not overmix.
Gently fold in the chopped walnut pieces or chocolate chips if using.
Fill muffin cups 2/3 of the way full. Bake 20-22 minutes or until toothpick inserted in the center of a muffin comes out clean. Let cool completely.
Makes 12-15 muffins.