Pierce potatoes with a fork; bake at 400° for 1 hour or until tender. Cool slightly. Peel potatoes; discard peels. Press cooked potatoes through a potato ricer into a large bowl. Weigh or lightly spoon flour into a dry measuring cup and spoon; level with a knife. Combine potatoes, flour, and 3/4 teaspoon salt. Stir well to form a dough.
Turn dough out onto a lightly floured surface. Knead until smooth. Divide dough into 4 equal portions, shaping each portion into a 20-inch-long rope. Cut each rope into 20 (1-inch) pieces; roll each piece into a ball. Working with 1 dough piece at a time (cover remaining dough to prevent drying), using your thumb, roll dough piece down the tines of a lightly floured fork (gnocchi will have ridges on 1 side and an indentation on the other). Place gnocchi on a baking sheet coated with cooking spray. Cover and set aside.
Bring 1 gallon water and 1 teaspoon salt to boil in a large Dutch oven. Add half of gnocchi to boiling water; cook gnocchi for 1 1/2 minutes or until done (gnocchi will rise to the surface). Remove gnocchi with a slotted spoon, and place in a colander to drain. Repeat procedure with remaining gnocchi.
Heat butter and olive oil in a medium skillet over medium heat. Add shallots to pan; cook for 10 minutes or until tender, stirring occasionally (do not brown). Stir in lemon rind, thyme, juice, and dash of salt. Combine butter mixture, gnocchi, cheese, and pepper in a large bowl; toss gently to coat.