Pour 4 tablespoons olive oil into a 3-quart saucepan set on medium-high heat and cook the 4 whole cloves of garlic and onion for 3-5 minutes. Reduce the heat to a simmer and cook until the onions are soft and begin to brown, about 10 minutes, stirring occasionally.
While the onions are cooking, put the tomatoes and their juices in a blender and process until smooth. Add the tomato puree to the onion mixture, raise the heat to high and bring to a boil for 5-8 minutes. Reduce the heat, add the basil and simmer for 25 minutes, stirring occasionally.
Sprinkle the eggplant cubes with 1/4 teaspoon of the salt and place in a colander set inside a bowl to catch the juices. Cover with a small plate, place a weight on top and drain for 15-20 minutes. Pat the eggplant dry with a towel and set aside.
Heat 3 tablespoons of the olive oil in a large nonstick saute set on high heat until sizzling, about 2 minutes. Add the drained eggplant, cook for 5 minutes, tossing several times, then remove to a bowl.
Add the remaining olive oil to the same pan and heat on high until sizzling , about 2 minutes. Cook the onion, peppers, and zucchini for 2 minutes, stirring occasionally. Add garlic, red pepper flakes, thyme, oregano, parsley, pepper and the remaining salt and cook for 3 minutes, until the vegetables have browned. Pour in the chicken stock and the browned eggplant and cook until reduced by half, about 2 minutes. Stir in the tomato sauce and cook until the sauce is thick, about 2 minutes. The vegetables may be cooled to room temperature and served, but the flavors will be more fully developed if refrigerated overnight, then returned to room temperature before serving.