Preheat oven to 350°F (175°C). Line a standard muffin tin with 12 paper liners.
In a medium bowl, sift together flour, baking powder, baking soda, ginger, cinnamon, nutmeg, and cloves. Set aside.
In a large bowl or stand mixer, combine melted butter, grated fresh ginger, and hot coffee on low speed.
Add molasses and brown sugar; beat until smooth.
Beat in the egg and yolks, mixing for 30 seconds.
Slowly add in the dry ingredients, mixing just until combined. Do not overmix.
Divide batter evenly among cupcake liners, filling each about ¾ full.
Bake for 14–16 minutes, or until a toothpick comes out clean.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.