Preheat the oven to 350 degrees F (175 degrees C). Bring a large pot of lightly salted water to a boil. Add pasta and cook until tender yet firm to the bite, 8 to 10 minutes. Drain.
While the pasta is cooking, mix ricotta cheese, 1/2 of the mozzarella cheese, 1/2 of the Parmesan cheese, eggs, parsley, salt, and pepper in a large bowl until well combined.
Ricotta cheese, mozzarella cheese, parmesan cheese, eggs, parsley, salt, and pepper mixed in a large bowl.
Combine pasta sauce and mushrooms in a medium bowl. Add remaining mozzarella and Parmesan cheeses; stir until well combined.
Stuff shells with ricotta mixture and place in a 9x13-inch baking dish. Pour pasta sauce mixture over the shells.
Bake in the preheated oven until edges are bubbly and the shells are slightly set, 35 to 60 minutes.