Preheat the oven to 300 degrees F (150 degrees C).
Set eight (5 1/2 ounce) ramekins into a large baking dish.
Stir together 1 1/4 cups sugar and water in a saucepan over medium heat; cook and stir until dark amber, about 10 minutes.
Quickly divide the caramel among the ramekins; set aside.
Whisk eggs, cinnamon, salt, cloves, ginger, allspice, mace, and 1/3 cup sugar together in a large bowl. Stir in pumpkin puree until smooth.
Heat milk in a saucepan over medium-low heat until it starts to gently bubble and steam.
Remove from heat.
Place vanilla bean seeds and pod in milk. Allow to soak for 10 minutes. Slowly strain hot milk mixture into the egg mixture and whisk to form a thin custard.
Divide the custard evenly among the ramekins, leaving about 1/4 inch at the top of each.
Fill baking dish with hot water to reach halfway up the sides of the ramekins. Cover the baking dish with heavy-duty aluminum foil.
Bake in the preheated oven until the flan is just set, 45 to 50 minutes.
Remove ramekins from hot water to cool completely. Cover and refrigerate until cold, at least four hours.
Run a knife around the inside edge of each ramekin and place an overturned plate on top. Invert and release the flan.
