Preheat the oven to 350°F (175°C) and lightly spray a 9x13-inch baking dish with nonstick spray.
Cook the jumbo pasta shells in a large pot of salted boiling water according to package directions until al dente; drain in a colander and set aside to cool slightly so they are easy to handle.
Heat olive oil in a large skillet over medium heat. Add the finely diced onion and sauté 3–4 minutes until softened.
Add the ground beef to the skillet with the garlic powder, kosher salt, and black pepper. Cook 8–9 minutes, breaking the meat into pieces, until browned and cooked through. Drain excess fat and let the beef cool slightly.
In a medium mixing bowl, combine the ricotta, 1½ cups of the shredded Italian cheese, Parmesan, whole egg and egg yolk, pesto, and chopped basil; season lightly with additional salt and pepper if desired. Fold the cooled beef into the ricotta mixture until evenly combined.
Stir half of the marinara sauce into the remaining beef in the skillet (or reserve half plain marinara) and season to taste; spread this sauce evenly across the bottom of the prepared baking dish.
Spoon a generous portion of the ricotta-beef filling into each cooked shell and place the stuffed shells in a single layer in the baking dish on top of the sauce.
Spoon the remaining marinara sauce over the shells, then sprinkle the remaining ½ cup of shredded Italian cheese evenly over the top.
Cover the dish with foil and bake for 25 minutes. Remove the foil and bake an additional 10 minutes, until the cheese is melted and bubbly.
Remove from the oven and let cool a few minutes, then garnish with fresh basil leaves before serving.
