Make the Cheesecake Filling: beat the filling ingredients together until smooth. Set aside.
Make the Pumpkin Muffins: In a large bowl, whisk together both flours, baking powder, baking soda, cinnamon, spices and salt. In a medium bowl, whisk the eggs and sugars together. Add the pumpkin, milk, oil and vanilla and whisk until blended. Pour the pumpkin mixture into the flour mixture and stir just until blended.
To assemble: preheat oven to 400°F (200°C). Line muffin pan with paper liners. Fill each muffin cup with one tablespoon of pumpkin batter and spread it to cover the bottom. Divide cheesecake filling among muffin cups (about 1 tablespoon per muffin). Top with the remaining pumpkin batter and spread to cover the cheesecake filling.
Bake at 400°F (200°C) for 5 minutes then reduce heat without opening the oven to 350°F (170°C) and bake for an additional 12-15 minutes, until a toothpick comes out clean. Cool in pans for 10 minutes then remove from the pans and cool on wire rack. Store muffins tightly covered in the refrigerator for up to 3 days, in the freezer for up to 3 months.