1. To make cream cheese filling: In a medium bowl, stir together the cream cheese and confectioners’ sugar until smooth. Add the vanilla, and stir to combine. Form the mixture into a 12-inch log on a piece of plastic wrap, wrap it, and freeze it for at least two hours.
2. Preheat oven to 350° F. Line a standard 12-cup muffin tin with paper liners and set aside.
3. To make the Pecan Streusel: In a medium bowl, use a fork to combine the flour, sugar, pecans, butter, and cinnamon. Set aside.
4. Whisk together the flour, cinnamon, nutmeg, cloves, baking soda, and salt in a large bowl.
5. In a medium bowl, whisk together the sugar, pumpkin, eggs, oil, and vanilla.
6. Pour the pumpkin mixture over the dry ingredients. Use a rubber spatula to gently combine the batter, mixing just until the dry ingredients are moistened.
7. Remove the cream cheese from the freezer, and divide it into 12 1-inch slices.
8. Scoop a small amount of batter into the muffin cups. Place 1 slice of the cream cheese log right in the center of each cup, then fill with the remaining batter.
9. Sprinkle the pecan streusel on top of each muffin. Press on the streusel lightly to make sure it adheres to the batter.
10. Bake until golden, about 20 to 25 minutes. Cool in the pan for about 5 minutes, and then remove muffins to a cooling rack to cool completely. Store in an airtight container in the refrigerator. Let them come to room temperature before serving.