Preheat the oven to 350 degrees F (175 degrees C).
Combine tomatoes, tomato juice, tomato paste, onion, parsley, salt, red pepper flakes, black pepper, thyme, and cloves in a large pot. Bring to a boil over high heat; reduce heat to low and let simmer for 1 to 1 1/2 hours.
Meanwhile, combine beef, crackers, eggs, Parmesan cheese, garlic, parsley, and thyme in a bowl. Form into large meatballs and place into a broiler pan.
Bake in the preheated oven until browned and no longer pink in the centers, about 30 minutes.
Transfer meatballs to sauce and continue to simmer, 2 to 2 1/2 hours more.
Bring a large pot of lightly salted water to a boil. Cook spaghetti in the boiling water, stirring occasionally, until tender yet firm to the bite, about 12 minutes. Drain.