Preheat oven to 350°F. Line muffin tins with cupcake liners or spray with nonstick cooking spray. Set aside.
To a medium mixing bowl, add flour, ginger, cinnamon, salt, nutmeg, baking soda, baking powder, and cloves. Whisk and set aside.
To a large mixing bowl, add brown sugar and butter and whisk until smooth and creamy.
Add molasses and whisk until combined. Add egg and egg yolks and whisk to combine.
Add milk, sour cream, and vanilla extract and whisk again, until combined.
Add dry ingredients from step 2 to the wet batter and whisk until just combined and no flour streaks remain.
Scoop the batter into the prepared muffin tins, filling them about 2/3 - 3/4 of the way up.
Bake in preheated oven for 20-22 minutes, or until a toothpick inserted in the center of a cupcake comes out with just a few moist crumbs, or clean.
Let cupcakes cool in the muffin tins for a few minutes, then remove the cupcakes to a cooling rack to finish cooling.