Preheat oven to 350°F. In a small bowl, stir together all ingredients for the cream cheese frosting, and set aside. In another small bowl, stir together all ingredients for the streusel topping, adding in pecans last. The batter should be slightly wet, but dry enough to form into small crumbles. If your consistency is off, add in one additional tablespoon of flour. Set aside.
In a large bowl, mix together flour, sugar, baking soda & powder, salt, nutmeg, cinnamon, ginger, and cloves until combined.
Make a well in the center of your dry ingredients. Pour in eggs, oil, milk, vanilla, and pumpkin puree. Whisk together the wet ingredients for about 30 seconds, then fold them into the dry ingredients until just combined.
Line a muffin tin with 12 large muffin cups. Carefully spoon 2 tablespoons of pumpkin batter into each muffin cup. With a second spoon, drop 1 tablespoon of cream cheese filling into the muffin cups. Top with another tablespoon of pumpkin batter. This should perfectly evenly distribute both mixtures so you have little to none left.
Last, top each muffin with 1 to 1 1/2 tablespoons of streusel by picking it up in your hands and crumbling the dough on top of each muffin. Once again, you should be left with little to know streusel once you top each muffin. Press down slightly on each muffin to set the streusel into the pumpkin batter.
Bake for 30 minutes, or until a knife inserted in the center of the a muffin comes out clean (there may be slight cream cheese residue, but as long as there is no pumpkin batter on your knife, they are ready!).