Preheat the oven to 400°F and line 2 baking sheets with parchment paper.
In a medium-sized shallow dish, whisk the eggs and almond milk.
In another medium-sized shallow dish, combine the panko, 1 cup Parmesan cheese, oregano, thyme, red pepper flakes, salt, and several grinds of pepper.
Dip the eggplant slices into the egg mixture and then into the panko mixture. Place onto the baking sheets, drizzle with olive oil, and bake for 18 minutes or until tender and golden brown.
In an 8x12 or 9x13-inch baking dish, spread ½ cup marinara, layer half the eggplant, and top with 1 cup of marinara and half the mozzarella. Repeat with the remaining eggplant, the remaining marinara, and the remaining mozzarella. Sprinkle with the remaining ¼ cup Parmesan cheese, drizzle with olive oil, and sprinkle with a few more pinches of sea salt. Bake for 20 minutes or until the cheese is nicely melted. Turn the oven to broil and broil for 2 to 4 or until the cheese is browned and bubbling.
Remove from the oven and top with fresh basil.