Preheat the oven to 350°F (175°C) and spray a 9x13-inch baking dish with cooking spray.
Heat the olive oil in a large skillet over medium heat. Add the diced onion and cook until softened, about 4–5 minutes.
Add the minced garlic, chopped portobello, and diced red pepper to the skillet; cook until the vegetables are tender, about 4–6 minutes. Remove from heat and let cool slightly.
In a large bowl, combine the ricotta, 1/4 cup shredded mozzarella, 1/4 cup grated Parmesan, and the egg; stir until smooth.
Add the drained, chopped spinach, dried basil, crushed red pepper, salt, and pepper to the cheese mixture and mix until evenly combined.
Fold the cooled mushroom, onion, and pepper mixture into the ricotta mixture.
Spoon about 1/2 cup marinara sauce into the bottom of the prepared baking dish and spread to cover.
Arrange the cooked jumbo shells in the dish in a single layer. Stuff each shell with the cheese and vegetable filling using a spoon.
Pour the remaining marinara sauce evenly over the stuffed shells, then sprinkle with the remaining 1/2 cup mozzarella and 1/4 cup Parmesan.
Cover the dish with foil and bake for 30 minutes. Remove the foil and bake an additional 5 minutes until bubbly and cheese is melted.
Let the dish rest for a few minutes before serving warm.