Preheat the oven to 350°F (175°C) and lightly spray a 9x13-inch baking dish with cooking spray.
Cook the jumbo pasta shells in a large pot of salted boiling water according to package directions until al dente. Drain and set aside to cool enough to handle.
Heat the olive oil in a large skillet over medium heat. Add the finely diced onion and sauté for 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 up the beef, until browned and cooked through. Drain excess fat and let the beef cool slightly.
In a mixing bowl, combine ricotta, 1½ cups of the shredded Italian cheese, Parmesan, the whole egg and extra yolk, basil pesto, and the chopped basil. Season with a little additional salt and pepper if desired, then fold in the cooled beef until evenly mixed.
Stir about half of the marinara sauce into the remaining beef in the skillet (or reserve half the sauce) and spread that sauce in an even layer across the bottom of the prepared baking dish.
Stuff each cooked shell with a generous spoonful of the ricotta-beef mixture and place the filled shells in a single layer in the baking dish.
Spoon the remaining marinara sauce over the stuffed shells, then sprinkle the remaining ½ cup of shredded Italian cheese evenly on 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 bubbling.
Let the stuffed shells rest a few minutes after baking, then garnish with fresh basil leaves and serve.