Preheat the oven to 375 degrees.
Cook the shells in boiling salted water per package instructions, stirring occasionally, until very al dente, about 9 minutes; drain. Place the separated shells on a baking sheet until needed. Side Note: Don't over cook the shells - they will finish cooking in the sauce. Meanwhile, heat the oil in a large oven proof skillet over medium-high heat.
Add the sliced mushrooms and cook, stirring occasionally, until they release their juices and are golden brown, about 5-6 minutes; season with sea salt and freshly cracked pepper, to taste.
Add the wine and cook, stirring often, until reduced by half, 2 minutes.
Add the spinach and cook, stirring constantly, until the spinach is wilted and most of the liquid has evaporated, about 4 minutes. Transfer mixture to a large bowl; set aside.
Heat the butter in the same oven proof skillet over medium-high heat.
Add the sliced garlic and crushed red pepper flakes and cook, stirring constantly, for 1-2 minutes, until fragrant and softened.
Add the marinara sauce and bring to a simmer over low heat. Cook, stirring occasionally until warmed through, about 4-5 minutes.
While the sauce is simmering, add the cottage cheese (or ricotta), Parmesan, mozzarella, and oregano to the bowl with the mushroom mixture; stir until well combined. Taste and season with sea salt and freshly cracked pepper, to taste.
Spoon about 2 tablespoons of the cheese mixture into each shell making sure not to over stuff the shells.
Nestle the stuffed shells into the simmering sauce. Cover with a lid and place into the oven to bake for 20 minutes.
Remove the lid and continue to cook for 5 minutes.
Remove from the oven. Serve with fresh parsley on top and Parmesan on the side. Enjoy.