Whisk flour, baking soda, and salt together in bowl. Set aside.
Grate fresh ginger.
MELT BUTTER, ADD SUGAR
Heat butter in 10-inch skillet over medium heat until melted. Lower heat to medium-low and continue to cook, swirling pan frequently, until foaming slows and butter is just beginning to brown, 2 to 4 minutes.
Transfer butter to large bowl and whisk in ground ginger, cinnamon, cloves, pepper, and cayenne. Let cool for a few minutes.
Add brown sugar, molasses, and fresh ginger to butter mixture and whisk to combine.
Add egg and extra yolk and whisk to combine.
COMBINE FLOUR MIXTURE, CHILL FOR 1 HOUR
Add the flour mixture into the butter mixture and stir until just combined. Cover dough with plastic wrap and refrigerate until firm, about 1 hour.
BAKE
Position oven racks to upper-middle and lower-middle spots and preheat oven to 300 degrees.
Line 2 baking sheets with parchment paper.
Place granulated sugar on a cutting board or plate. Divide dough into heaping teaspoon portions and roll dough into balls. Roll balls in sugar to coat. Place balls on prepared baking sheets, 20 dough balls per sheet.
Place 1 sheet on upper rack and bake for 15 minutes. After 15 minutes, transfer top sheet to lower rack, rotating 180 degrees, and place second sheet of dough balls on upper rack. Continue to bake until cookies on lower tray just begin to darken around edges, 10 to 12 minutes longer. Remove lower sheet of cookies and shift upper sheet to lower rack and continue to bake until cookies begin to darken around edges, 15 to 17 minutes. Slide baked cookies, still on parchment, to wire rack and cool completely before serving. Cool baking sheets slightly and repeat step 2 with remaining dough balls.