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If necessary, cook the bacon according to one of my easy methods listed below. Once cool enough to handle, chop into rough pieces and set aside.
Preheat the oven to 350 degrees F. In a large skillet, heat 2 teaspoons olive oil over medium high. Add onions and sauté just beginning to soften, about 3 minutes. Reduce heat to medium low and continue to cook onions until caramelized and tender, stirring occasionally. Let the onions cook for at least 10 additional minutes, or up to 30 minutes as you prepare the rest of the recipe.
In a deep, wide saucepan, combine pumpkin, stock, and milk, then bring to a boil over medium-high heat. Reduce heat to medium and simmer until sauce thickens slightly, about 8 minutes. Remove from heat, then stir in mustard, salt, pepper nutmeg, and cayenne.
Meanwhile, bring a large pot of water to a boil. Add noodles and 1 tablespoon kosher salt, then cook just until al dente according to package instructions. Drain, then transfer noodles to a large bowl. Pour pumpkin sauce over the top, then stir in the cheddar, Greek yogurt, and 2 tablespoons Parmesan. Fold in all of the caramelized onions and reserved bacon.
Lightly coat a 9-inch square, deep baking dish or a 2-quart casserole dish with cooking spray. Transfer the pumpkin noodle mixture to dish. In a small bowl, combine breadcrumbs, remaining 2 tablespoons Parmesan, and remaining 1 teaspoon olive oil. Sprinkle the mixture evenly over the noodles. Cover dish with foil and bake 20 minutes. Remove foil and continue baking until lightly browned and crisp on top, 30 to 35 minutes more. Serve immediately.