Preheat the oven to 375°F.
Combine the tomatoes, onion, squash, eggplant, and sweet potatoes in a large bowl and season to taste with pepper. Sprinkle the vegetables with 1 to 2 tablespoons of water, enough to lightly and evenly coat them. Toss gently with herbs, lemon juice, and garlic.
Arrange the vegetable slices in a baking dish in rows in the following order: sweet potato, tomato, eggplant, tomato, sweet potato, squash, onion, tomato, eggplant, tomato. Layer them in such a way that they are stacked tightly on a diagonal.
Sprinkle the top with the extra herbs and pour any juice left in the bowl over the vegetables. Cover tightly with foil and bake for 1 hour. Remove the foil and continue baking for another 30 minutes, until the vegetables are completely tender and slightly browned around the edges.