Preheat the oven to 350˚F and line a 10 x 12inch pan with parchment paper.
In a heavy based pan lightly toast the pecans (whole) for 5 to 10 minutes. Do not allow to burn. When cool enough to handle chop them finely and set aside.
In a large bowl sift together the flours, baking powder, baking soda, salt, pumpkin pie spice and cinnamon. Stir in the sugars and mix well. Next stir in 1 cup of the chopped pecans, reserve & set aside the extra ¼ cup to sprinkle on top of the finished cake.
In a medium sized bowl or jug, mix together the applesauce, oil, milk, pumpkin puree, flax meal, water and vanilla extract. Whisk this mixture together and leave it to sit for 5 to 10 minutes.
Make a well in the center of the dry mixture and pour in the wet mixture. Mix until just combined and then scrape the batter into the lined pan. Bake in the center of the oven for 30 to 40 minutes. Insert a wooden toothpick in the center of the cake to ensure its cooked fully. Remove from the oven and allow to cool down in the tray.
When fully cool remove from the pan and transfer to a serving plate. Decorate with cream cheese frosting and the remaining ¼ cup of chopped pecans if desired. Refrigerate until ready to serve.