Preheat the oven to 350°F. Spoon 1½ cups of the marinara sauce over the bottom of a 9x13-inch casserole dish.
Bring a medium pot of water to a boil. Add the shells, reduce the heat slightly, and boil, uncovered, for 10 to 13 minutes or until al dente (tender with some bite).
Remove the shells from heat and drain in a colander. Let them cool in the colander until they are a comfortable temperature to handle.
While the pasta is cooking and cooling, add to a food processor the tofu, 1 handful of spinach, lemon juice, miso paste, nutritional yeast, plant-based milk, Italian seasoning, kosher salt, and black pepper. Pulse until the spinach is broken down. Add the rest of the spinach and continue pulsing until the ricotta has a creamy, textured consistency. Taste and add an additional squeeze of lemon juice if desired, but go slowly—adding too much can tip the ricotta into sour territory.
Scoop the ricotta into the cooled shells. Carefully place the stuffed shells in the prepared casserole dish. Drizzle a couple spoonfuls of marinara sauce over the shells if you prefer the filling to be visible (reserve the rest of sauce for serving). Alternatively, spoon all the remaining sauce over the stuffed shells.
Cover the casserole dish with aluminum foil. Bake for 40 to 45 minutes, or until the shells are cooked through.
Enjoy as is or garnished with fresh basil leaves and/or vegan Parmesan. Serve any remaining marinara sauce warmed at the bottom of the serving bowls or plates or on the side.