Preheat oven to 350°F. Line two 12-cup muffin tins with paper liners or spray with nonstick cooking spray. Set aside.
In a medium bowl, whisk together the flour, baking soda, salt, cinnamon, nutmeg, ginger, cloves, and baking powder.
In a large bowl, beat the eggs, sugar, pumpkin, oil, orange juice, molasses, and vanilla until fully combined.
Add the dry ingredients to the wet ingredients and mix just until combined. Be careful not to overmix.
Transfer about half of the batter to a separate bowl. Add the cocoa powder to that batter and gently stir until combined.
Add alternating spoonfuls of the plain pumpkin batter and chocolate pumpkin batter into each muffin cup, filling each about ¾ full.
Using a toothpick or thin skewer, gently swirl the batters together with a figure-8 or S-shaped motion. A few gentle swirls are all you need; too much swirling will blend the batters together instead of creating a marbled look.
Bake for 20 to 25 minutes, or until a toothpick inserted into the center comes out with a few moist crumbs, but no wet batter.
Let the muffins cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.