Pour 6 cups of the chicken stock along with 2 teaspoons of the kosher salt into a large stockpot and bring it to a boil over medium heat. Add the spaghetti and the remaining stock if needed to just cover the pasta.
Cook for 12 to 14 minutes or until just tender, stirring occasionally.
While the stock comes to a boil start the sauce by melting the butter with the olive oil in a separate stockpot or deep pan over medium heat. Add the chopped onions, bell peppers, mushrooms and season with the black pepper.
Cook, stirring occasionally until the vegetables are tender, about 10 to 12 minutes.
Toss in the flour, ½ teaspoon of the remaining kosher salt and the red pepper flakes then stir to coat the vegetables. Continue cooking for about 3 minutes.
Stir in the half and half and cook for about 2 to 3 minutes to thicken slightly. Check for seasoning and add the remaining ½ teaspoon of kosher salt if needed. Combine the sauce with the pasta and chicken stock along with the chopped tomatoes.
Remove the pan from the heat and stir in 1-½ cups of the shredded cheese and the chicken.
Pour the pasta into a large baking dish that has been coated with a cooking spray. Sprinkle the remaining cheese over the top.
Loosely cover the dish with foil and bake in a 350-degree for about 20 to 30 minutes or until hot and the cheese has melted.