Bring a large pot of salted water to boil. Cook the pasta shells as per the package directions. Drain, reserving 1/4 cup of the cooking liquid. Cool the pasta shells in cold water and drain well again. Set aside.
Set 24 of the shrimp aside in a small bowl and refrigerate until needed. Coursely 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°F Pour the jar of pasta sauce into a large, wide baking dish; stir in the reserved pasta cooking liquid. Spoon 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 the Parmesan cheese. Cover with foil and bake 30 minutes. Uncover and bake 15 minutes more, or until the tops are golden and the sauce is bubbling.