Bring a large pot of water to boil. Cook the pasta shells as per package directions; reserve 1/4 cup of the cooking liquid. While the pasta cooks, set 24 of the shrimp in a small bowl and refrigerate until needed. Coarsely chop the remaining shrimp and place in a medium bowl. Mix in the ricotta, pesto, eggs,1/2 cup mozzarella cheese, flour, salt, pepper and nutmeg.
Preheat the oven to 350 degrees F. When the shells are cooked, drain well, cool in cold water, and drain well again. Pour the pasta sauce into a large, wide casserole; stir in the reserved pasta cooking liquid. Divide, spoon and stuff the ricotta/shrimp mixture into the pasta shells and set them on top of the pasta sauce. Set a whole shrimp on top of each shell. Sprinkle the shells with the 1 cup mozzarella cheese and Parmesan. Cover and bake 30 minutes. Uncover and bake 15 minutes more,or until the tops are golden and the sauce is bubbling.