In a medium bowl, whisk together both flours, the baking soda, salt and spices.In a large bowl, whisk together the sugar, molasses, oil, and one of the eggs until combined. Add the other egg and whisk well. Whisk in the pumpkin and vanilla. Stir in the flour mixture in two batches, alternating with the buttermilk, just until combined.
Pour the batter into the prepared muffin pan, filling each one about two-thirds full, and sprinkle the surface of each with the pumpkin seeds. Tap the pan on the counter a few times to remove any air bubbles. Bake until a wooden toothpick inserted in the center of one of the muffins comes out clean, about 20 minutes.
Let cool on a wire rack for 15 minutes. Run a knife around the muffins to loosen them and unmold. Enjoy warm or let cool completely before storing in an airtight container in the refrigerator for up to 3 days or in the freezer for up to 3 months.