Make the 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 in the plastic wrap and then again in foil, and freeze for at least two hours, or until firm.
Make the Streusel: In a medium bowl, whisk together the flour, sugar and cinnamon. Stir in the pecans, then use a fork to mix in the melted butter, ensuring that all of the ingredients are moistened. Refrigerate while you prepare the muffins.
Make the Muffins: Preheat oven to 350 degrees F. Line a standard 12-cup muffin tin with paper liners; set aside.
In a large bowl, whisk together the flour, cinnamon, nutmeg, cloves, ginger, allspice, baking soda and salt.
In a medium bowl, whisk together the sugar, pumpkin, eggs, oil, and vanilla extract.
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.
Remove the cream cheese from the freezer, and divide it into 12 1-inch slices.
Scoop 2 to 3 tablespoons of batter into the muffin cups. Place 1 slice of the cream cheese log in the center of each cup, then divide the remaining batter evenly between the muffin cups, ensuring that the cream cheese is completely covered.
Sprinkle the pecan streusel on top of each muffin. Press on the streusel lightly to make sure it adheres to the batter.
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 for up to 4 days. Let them come to room temperature before serving, or warm briefly in the microwave to take the chill off. The muffins can be wrapped in plastic wrap and frozen for up to 2 months.