Preheat the oven to 375°F and bring a large pot of water to a boil.
Meanwhile, heat the oil in large, deep skillet over medium-high heat. Add the ground beef, onions, and garlic and cook, breaking up the meat into very small pieces with the edge of a spoon, until cooked through and no longer pink. Drain off excess fat and return to the skillet.
Pour in the white wine and cook, stirring, until it has reduced by half, 3 to 4 minutes.
Reduce heat to low and add the marinara, 1½ teaspoons salt, 1/2 teaspoon black pepper, oregano, and basil. Stir to combine and cover. Set aside.
When the water is boiling, add the jumbo shells and cook until al dente, according to package directions.
While the pasta cooks, make the filling. In a medium mixing bowl, combine the ricotta, parsley, egg, lemon zest, Parmesan, 1 cup of mozzarella, 1/2 teaspoon salt, and 1/2 teaspoon of black pepper. Mix until very well combined.
When the shells are done, drain and lightly rinse with cool water.
In the bottom of a 13x9 baking dish, spread 1/2 of the meat mixture into an even layer. Gently stuff each shell with about 2 tablespoons of the ricotta mixture and place the stuffed shells in a single layer, seam side up, in the baking dish. Once all of the shells are filled, pour the remaining meat mixture over the top in an even layer. Sprinkle with the remaining mozzarella.
Cover tightly with foil, transfer to the oven, and bake for 25 minutes. Remove the foil and continue to bake until the cheese is lightly browned and bubbly, about 10 minutes.
Remove from the oven and let cool for 5 minutes. Garnish with fresh basil and serve!