In a large bowl, whisk together the flour, baking soda, salt, ground ginger, cinnamon, cloves, and cocoa powder. In the bowl of a stand mixer fitted with the paddle attachment, or using a hand mixer, beat the butter and brown sugar on medium speed until light and fluffy, 2 to 3 minutes.
Beat in the fresh ginger and egg yolks until combined. Add the molasses and vanilla and then add the flour mixture and mix on low speed just until no flour pockets remain.
Stir in the chocolate and candied ginger. Cover and refrigerate the dough until firm, at least 3 hours and preferably overnight.
Preheat the oven to 350°F (177°C). Line a rimmed baking sheet with parchment paper.
Place the granulated sugar in a bowl. Pinch off pieces of dough about the size of a golf ball (about 1 1/2 ounces | 43 g). Roll each ball in sugar and place on a separate unlined baking sheet.
Freeze for 10 minutes. Roll each dough ball in the sugar again.
Working in batches, place the dough balls 2 inches (5 cm) apart on the prepared baking sheet. Stash the remaining sugar-coated dough balls in the refrigerator while the first batch bakes. (Alternatively, you can freeze the unbaked dough balls on a baking sheet until solid, pop them in a resealable bag, and bake them whenever craving strikes.)
Bake the cookies, rotating the pan after 5 minutes, until the tops begin to crack and the edges are just set, 10 to 14 minutes. Be careful not to overbake.
Let the cookies cool for about 5 minutes on the baking sheet, then transfer to a cooling rack to cool completely.