Chewy Ginger-Rye Cookies

Whisk all-purpose flour, baking soda, cinnamon, cloves, ¾ cup rye flour, 2 tsp. ground ginger, and 1 tsp. salt in a medium bowl to combine; add crystallized ginger and toss until coated and evenly distributed. Whisk molasses, brown sugar, and ¾ cup melted butter in a medium bowl to combine. Add egg yolks and whisk just until egg yolks are absorbed but mixture is still very dark, about 10 seconds. Add dry ingredients and fold until no streaks of flour remain. Let sit, uncovered, at room temperature 30 minutes (batter will thicken as it sits).
Meanwhile, place a rack in middle of oven; preheat to 375°F. Whisk raw sugar, remaining 6 Tbsp. rye flour, remaining 1 tsp. ground ginger, and remaining ¼ tsp. salt in a small bowl to combine. Add remaining room-temperature butter and smash together until mixture resembles clumpy wet sand; this is your streusel topping.
Using a 1-oz. ice cream scoop, portion out dough (about 2 Tbsp. each) and roll into balls between your palms. Working one at a time, toss balls in streusel mixture to coat and place on 2 parchment-lined baking sheets, spacing 3" apart. Bake 1 sheet of cookies until they have spread and are slightly cracked and just set around the edges and streusel is lightly browned, 8–10 minutes. Let cool 10 minutes on baking sheet. Transfer to a wire rack and let cool completely. Bake remaining sheet of cookies.
Do Ahead: Dough can be rolled into balls 2 weeks ahead. Freeze on a baking sheet; transfer to resealable plastic freezer bags. Let sit at room temperature 30 minutes before rolling in streusel and baking.