Heat oven to 425 degrees. Spray 13x9 pan liberally with non-stick spray. Start a pot of 5 qt water with liberal salt for the penne.
Cook bacon until crisp over medium heat in a large non-stick skillet. Drain bacon over paper towels and reserve 3 TBSP fat in pan.
Salt and pepper chicken pieces. Cook chicken breast pieces in the bacon fat for about 4 minutes, until no longer pink in the center. Reserve chicken and tent with foil.
Add enough olive oil to coat pan; add squash, salt, pepper and sage. Cover pan and stir occasionally for 5-7 minutes, until squash is semi-soft. Add onion and continue to cook for 3-5 minutes, until onion is translucent. Add garlic, red pepper, and spinach to skillet and cook until spinach is wilted, 3-4 minutes.
Do not cook your penne until al dente; it will continue to cook in the oven. Only cook for about 7 minutes.
In a seperate saucepan cook flour over medium heat, gradually adding milk and whisking continuously until boiling. Boil for two minutes or until thickened; remove from heat and add cheese, stirring until melted.
Add flour/milk/cheese mixture to pasta; add pasta to squash mixture. Add more milk if mixture is too thick. Spread mixture into 13x9 pan; sprinkle more cheese on top if desired. Cook in oven 15-20 minutes or until cheese is browned and bubbling. Let cool for 10-15 minutes; serve.