Bring a large pot of water to a rolling boil over high heat. Add salt, then add the jumbo shells. Cook according to the package directions until al dente and still firm enough to hold their shape without splitting or cracking. Drain and rinse briefly with cool water to stop the cooking. Arrange the shells on a tray with enough space between them so they do not stick together.
Place the vegan ricotta in a large bowl. Stir in the chopped spinach, chopped parsley, oregano, lemon zest, crushed red pepper flakes, minced onion, and garlic.
Preheat the oven to 375°F (190°C). Spread a portion of the marinara sauce across the bottom of a baking dish to create an even layer.
Fill each cooked shell with the ricotta and spinach mixture using a spoon. Arrange the filled shells in the baking dish in a single layer with the open sides facing upward.
Spoon the remaining marinara sauce evenly around the shells. Drizzle olive oil lightly over the filled shells.
Transfer the dish to the oven and bake at 375°F (190°C) until the sauce is bubbling and the shells are heated through, 25 minutes.
Remove the dish from the oven and garnish with grated vegan parmesan, basil leaves, and chopped parsley.