Place the shells in a 13'' x 9'' baking dish that has been sprayed with cooking spray.
Sauté the bacon in a medium-size saucepan until browned, about 10–12 minutes. Remove the bacon to a paper towel-lined plate to drain.
Remove some of the bacon fat from the pan, leaving about 1/4 cup. Add the onions and sauté until translucent, about 6–8 minutes. Return the bacon to the pan. Stir in the flour then add the chicken stock and the milk.
Bring the mixture to a simmer and let it thicken, stirring constantly. Add in the pumpkin purée, rosemary, thyme, Parmesan, salt, and pepper. Bring the mixture back up to a simmer.
Pour the sauce evenly over the shells and top with the grated Fontina cheese.
Place the pan on the middle rack in the preheated oven and bake for 35–40 minutes, or until bubbly and browned on top.
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