Slice the eggplant into ½-inch slices. Lay some paper towels or a clean dishtowel on a large baking tray. Lay the slices out on the tray and sprinkle them with about ½ teaspoon of salt. Let them sit for 10 minutes.
During that time, mix the milk with the flour in a bowl and set aside.
Mix the breadcrumbs, nutritional yeast, Italian seasoning, garlic powder and salt and set aside.
When the eggplant is ready, take some paper towels and pat over the tops of the eggplant to pick up an excess water. Then dip each slice into the flour mixture, then into the breadcrumb mixture. Place each slice on a baking tray lined with parchment paper.
Bake the eggplant for 20 minutes.
While that is baking, mix 2 cups of the mozzarella and the Parmesan.
Spread ¼ cup of sauce in a 9x13-inch baking dish. Add a layer of cooked eggplant, then half of the cheese mixture. Now repeat sauce, eggplant, and cheese and top with the remaining sauce.
Bake for 20 minutes with foil on. Then remove the foil and add the remaining mozzarella. Cook for 5 more minutes.