Whisk together flour, cinnamon, ginger, cloves, baking soda, baking powder, and salt in a medium bowl.
Whisk together pumpkin, melted butter, brown sugar, egg, vanilla, and 1 tablespoon bourbon in a large bowl.
Add flour mixture to pumpkin mixture and stir, using a rubber spatula, until just combined. Cover with plastic wrap and refrigerate for at least 1 hour or up to over night.
Heat oven to 350°F (176ºC) with rack set in middle position. Line two baking sheets with parchment paper.
Using a tablespoon measure and lightly moistened hands, roll dough into balls; place evenly on prepared baking sheets, about 20 per sheet. Gently flatten dough balls with slightly dampened fingers to about ½-inch thick.
Bake cookies, one sheet at a time, until set and tops spring back when gently pressed, 12–14 minutes. Let cookies cool on sheets 5 minutes, then transfer to a wire rack to cool completely.
Beat together cream cheese and butter using a hand-held mixer or in a stand mixer fitted with a whisk attachment until smooth.
Add confectioners’ sugar, 2 tablespoons bourbon and a pinch of salt. Mix until smooth, adding more confectioners’ sugar as needed to create a stiff yet spreadable consistency. Refrigerate until ready to use.
Spread scant 1 tablespoon cream cheese filling onto bottom side of half of the cookies; sandwich with remaining cookies, bottom side down, pressing gently.
Dust whoopie pies with additional confectioners' sugar before serving, if desired.