Heat oven to 400. Cook pasta for 2 minutes less than the time on package directions. (Under cook as it will cook more in oven.) Drain and transfer to a large bowl. Add 3 tablespoons of the butter to the pasta and toss to coat.
In Medium sauce pan heat the remaining 1 tablespoon of butter over medium heat. Add the onion and cook until tender and starting to color. (about 7 minutes) Add the carrots and squash and cook until carrots are tender. (about 5 minutes.)Add tomatoes and cook 1 minute.
Transfer the vegetables to the bowl with the pasta. Add 2 cups of the cheddar cheese, the sour cream, milk eggs, salt and pepper and stir until well combined. Transfer the mixture to a 9x9 inch baking dish and scatter the remaining 1 cup of cheddar on top. Top dish with the popcorn.
Cover with foil and bake until pasta is hot and top is lightly crusted, uncovering during last 10 minutes, about 25 minutes of baking. Serve.