In a large bowl, use your hands to break up the tomatoes, squeezing them into 1/2-inch pieces. Set aside.

Place the pancetta in a large, heavy-bottomed saucepan or Dutch oven over medium-low heat. Cook gently until the pancetta releases its juices and browns, about 15 minutes. Remove with a slotted spoon and reserve.

To the rendered fat in the pan, add the olive oil and, when hot, the onions and 1/2 teaspoon salt. Cook until soft and golden, about 5 minutes. Add the garlic and cook just until it releases its fragrance, about 1 minute. Add the red pepper flakes and oregano, cook for a minute or two, and then add the red wine. Cook until the wine is almost evaporated, scraping up any browned bits from the bottom of the pan. Return the pancetta to the pan, along with the tomatoes and their juices, the carrots, and the basil. Bring to a boil, then reduce the heat to low and simmer gently, stirring frequently, until thickened and reduced by one-half to two-thirds, about 5 hours.

When the sauce has thickened and reduced, remove the carrots and basil, and puree to the desired smoothness using an immersion blender. Stir in the parsley.

Preheat the oven to 400 degrees F.

Using a mandolin, thinly slice the zucchini and squash; about 1/4 inch. Set aside.

In a large baking dish, pour tomato sauce and spread evenly over the bottom, about 3 cups. Alternating between each vegetable, overlapping slightly, place the zucchini and squash into the sauce. Work your way around the dish starting from the outside in until filled. Drizzle with a little olive oil and season salt and pepper.

Bake for 45 minutes, or until vegetables are tender and the top is golden brown. Garnish with fresh thyme and serve immediately.