Place oven rack on the middle setting and preheat the oven to 350ºF. Line a 12-count muffin tin with cupcake liners. Set aside.
In a large bowl whisk together the flour, ginger, cinnamon, nutmeg, cloves, allspice, salt, pepper, baking soda, and baking powder. Set aside.
In a large bowl with a handheld mixer, or the bowl of a stand mixer fitted with the paddle attachment, cream the butter and brown sugar together until light and fluffy. Add the egg and allow to incorporate. Add the molasses and beat again on medium speed until everything is incorporated, scraping down the sides and bottom of the bowl with a spatula as needed.
Add the flour mixture in three additions alternating with the milk, starting and ending with the flour mixture. Mix until smooth.
Spoon batter evenly into the cupcake liners filling 1/2 to 2/3 of the way full (I like to use an ice cream scoop with a trigger-- one scant scoop full). Bake for 14-16 minutes or until a toothpick inserted in the center comes out clean. Allow to cool in the pan for a few minutes, then transfer to a wire cooling rack to cool completely.
CREAM CHEESE FROSTING
In a large bowl with a handheld or the bowl of a stand mixer fitted with a paddle attachment, beat the cream cheese and butter together on high speed until smooth and creamy. With the mixer on low, add the powdered sugar, vanilla, and salt.
Increase mixer speed to medium-high and beat for 2 minutes.