In a large dutch oven, begin browning the ground beef. Once it begins to break up and is about halfway cooked add in the diced pepperoni. Continue cooking and breaking up the beef. Once the beef is cooked and the fat has rendered from the pepperoni, drain the fat. Add in the remaining sauce ingredients – basil, salt, tomato juice, tomato paste, and sugar. Simmer for about 30 minutes.
While the sauce is simmering, cook the noodles according to package directions. Rinse with cold water.
Make the cheese filling by stirring together the cottage cheese, parmesan, parsley, eggs, and salt.
Place a small amount of sauce in the bottom of each pan. Add a layer of noodles (trimming with kitchen shears to fit the pan), ½ of the cheese filling, just shy of ½ the mozzarella, a layer of noodles (optional), and ½ of the meat sauce. Repeat the layers. Sprinkle with remaining mozzarella cheese.
Bake at 375 degrees for 30 minutes until hot and bubbling around the edges. Allow to cool for about 10 minutes before slicing.
For any extra pans, cover tightly with aluminum foil and freeze. Thaw about 24 hours before baking and add 20-25 minutes to the cooking time.