In a large bowl, combine bread crumbs and milk and let it rest for 10 minutes.
Line a baking sheet with foil and place a wire rack on top. Lightly grease with cooking spray. (If you don't have a wire rack the meatballs can be placed right on the foil.)
Preheat oven to 450 degrees F.
To the bread crumbs, add eggs, cheese, onion, garlic, basil, oregano, parsley, salt, and peppers. Stir and then mix in the ground beef with hands until evenly combined.
Roll the meat mixture into 20 2-inch balls.
Place the 1/3 cup flour in a small bowl and then roll the meatballs in the flour and place on wire rack.
Bake for 30 minutes.
For the Sauce:
Heat oil over medium high heat in a large Dutch oven. Add onion and saute until tender. Add garlic, red pepper flakes, basil, parsley, and oregano and cook for 30 seconds. Add the crushed tomatoes, tomato sauce, bay leaves, salt, pepper, and sugar. Bring to a simmer, reduce heat to low and simmer uncovered for 10-15 minutes to slightly thicken (use a splatter screen to reduce splattering). (Add baking powder if sauce tastes too acidic.)
Gently add the meatballs to the sauce. Cover with lid and place in the oven for 30 minutes at 300 degrees F.
For the Pasta:
When 15 minutes remain, cook pasta according to directions on package.
Serve meatballs and sauce over pasta and sprinkle with freshly grated Parmesan cheese.