2 tbsp. chopped fresh cilantro (plus more for garnish)
1 28-oz. can crushed tomatoes
Sour cream, for serving
Lime wedges, for serving
Preheat oven to 350º.
In a large pot of salted boiling water, cook pasta according to package directions until al dente. Drain and return to pot.
Cook beef: In a large skillet over medium heat, add ground beef, cumin and chili powder and cook until beef is no longer pink. Drain fat, then return skillet to heat and stir in tomatoes, most of the cheddar (reserve some for topping) and most of the Monterey Jack (reserve some for topping). Season with salt and pepper. Cook, stirring often, until cheese has melted, then remove from heat.
Make sauce: In a medium sauce pan over medium heat, heat olive oil. Add onion and cook until tender, about 5 minutes. Add garlic and jalapeño and cook until fragrant, about 1 minute more. Add crushed tomatoes and season with salt and pepper. Bring mixture to a boil then reduce heat and simmer, 10 minutes. Stir in cilantro.
Spoon a thin layer of sauce in the bottom of a large casserole dish. Stuff meatball mixture into shells and arrange stuffed shells on top of sauce, side by side. Spoon remaining sauce over shells and sprinkle with cheese.
Bake until cheesy is melted and bubbly, 18 to 20 minutes. Garnish with cilantro and serve with sour cream and lime wedges.