Bring a large pot of salted water to a boil. Cook jumbo shells until just al dente. Drain and let cool slightly.
In a large skillet over medium-high heat, cook ground beef with a little salt and pepper until browned and caramelized.
Add chopped onion and cook 3–4 minutes until softened. Stir in garlic for 1 minute.
Add tomato paste and cook 1–2 minutes to deepen the flavor.
Stir in tomato sauce, diced tomatoes with juices, water, Italian seasoning, and optional red pepper. Simmer 10–15 minutes, then taste and adjust seasoning.
In a mixing bowl, combine ricotta, egg, 1 cups mozzarella, 1/3 cup Parmesan, garlic powder, herbs if using, plus a pinch of salt and pepper.
Spread a thin layer of the meat sauce in the bottom of a 9×13 baking dish.
Fill each cooked shell generously with the ricotta mixture and arrange the shells in the dish.
Top each shell with a spoonful of the meat sauce over the ricotta mixture.
Spoon the remaining red sauce over the top of all of the stuffed shells.
Sprinkle the remaining mozzarella and Parmesan evenly over the top.
Cover tightly with foil and bake at 350°F for 25 minutes.
Remove foil and bake 10–15 minutes longer, or until the cheese is melted, bubbly, and lightly golden. Optional: broil 1–2 minutes for more browning.
Rest 5 minutes before serving. Garnish with fresh basil or parsley if desired.