Heat the oven to 400°F (204°C) and line a standard 12-cup muffin pan with paper liners.
Whisk the eggs, brown sugar, pumpkin purée, molasses, vanilla, oil, and milk in a large bowl.
Whisk the flour, baking powder, pumpkin pie spice, cinnamon, ginger, and salt in a separate bowl.
Fold the dry ingredients into the wet ingredients just until combined.
Fold in the pecans, chopped chocolate, and chocolate chips without overmixing.
Fill each liner completely to the top and add optional toppings.
Bake for 22–24 minutes, until a wooden pick comes out clean or with melted chocolate but no wet batter.
Cool in the pan for 15 minutes, then transfer to a wire rack.