Preheat oven to 350 degrees F. Line two baking sheets with parchment paper.
In a large bowl, mix together the flour, salt, baking powder, baking soda, cinnamon, ginger, and cloves together and set aside.
In the bowl of a stand mixer fitted with the paddle attachment, mix the brown sugar and oil together until combined. Add the pumpkin puree and mix to combine thoroughly. Add the eggs and vanilla and mix until combined.
Add the flour mixture to the pumpkin mixture and mix until completely combined.
Drop heaping tablespoons of the dough onto the prepared baking sheets, about 1-inch apart. Bake for 10 to 12 minutes, until the cookies are just starting to crack on top and a toothpick inserted into the center of the cookie comes out clean. Remove from oven and let cool completely on the pan while you make the filling.
Sift confectioners sugar into a medium bowl and set aside.
In the bowl of an electric mixer fitted with the paddle attachment, beat the butter until it is completely smooth, with no visible lumps. Add cream cheese and beat until combined.
Add confectioners sugar and vanilla and beat until smooth.
Turn half of the cooled cookies upside down, flat side facing up.
Use a tablespoon to drop a large dollop of filling onto the flat side of the cookie. Place another cookie, flat side down, on top of the filling. Press down slightly so that the filling spreads to the edges of the cookie. Repeat until all cookies are used. Place whoopie pies into the refrigerator for 30 minutes to firm up before serving.