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To make the filling, whip the softened cream cheese with a whisk or hand mixer until very smooth and creamy. Whip in the egg yolks, sugar, vanilla, rum, nutmeg, and cinnamon. (Can be made a day ahead and chilled in the refrigerator, if desired.)
To make the muffins, heat the oven to 375°F. Line a 12-cup muffin pan with paper liners.
Whisk together the melted butter, eggs, and pumpkin. Add the brown sugar and molasses and whisk until smooth. Dump in the flour, baking soda, salt, ginger, cinnamon, cloves, and black pepper, and whisk until just combined. The batter will be relatively thick.
Take out about 3/4 cup batter and set aside. Divide the remaining batter evenly between the prepared muffin cups. They will be nearly full. Use a spoon to poke a deep cavity in the center of each muffin, and fill this cavity with the chilled cream cheese mixture. Put a tablespoon of the reserved batter on top of the filling.
Bake for 25 minutes or until the filling in the center is puffed and set, just barely golden brown, and the muffin batter is fully cooked through. Cool at least 5 minutes before eating.
If you're feeling celebratory, serve with a squirt of whipped cream and a sprinkle of nutmeg.
Store for up to 5 days at room temperature in a covered container.