In a large bowl, whisk together the flour, salt, baking soda, baking powder and spices. Set aside.
In a mixing bowl, whisk the sugars, molasses, oil and melted butter together. Add the pumpkin puree and combine thoroughly. Add the eggs and vanilla and whisk until combined. Pour the flour mixture over the wet ingredients and slowly whisk to combine. Do not overmix. Slowly stir in chocolate chips.
Preheat oven to 350 degrees. Prepare baking sheets lined with parchment paper or a Silpat.
Place entire bowl in the refrigerator to chill for 20 minutes while oven preheats, then use a cookie scoop to place round cookies in 2-inch circles on prepared sheets. Bake for 13-15 minutes or until cookies look done.
Beat cream cheese, butter, salt and cinnamon until lump-free and smooth. Gradually add sugar until well combined. Add vanilla until just incorporated. Once cookies are cooled, fill centers with cream cheese icing.