Cook the bacon and remove from pan, reserving the drippings.
Saute the onions and fresh Thyme on a medium heat in the bacon drippings, till the onions are translucent, but watch the heat. Fresh Thyme burns easily. Then, add 1/3 cup of the Chicken stock and simmer the onion/thyme mixture, covered, to further bring out the flavor, until all the liquid cooks off.
Using a large, heavy saucepan, or stockpot over medium heat, blend the olive oil and flour to create a sauce, but turn down the heat, flour burns easily. Stir constantly until browned and bubbly. Mix in garlic, and cook about 1 minute.
Gradually stir in the chicken broth and red wine vinegar into the sauce mixture. Bring to a gentle boil to allow the vinegar to cook down but still stirring constantly.
Now add in the fresh tomatoes, canned tomatoes, okra, Rotel, red chile peppers, cooked rice, Cajun seasoning, and the Onion/Thyme mixture to the stockpot and simmer everything for at least 40 minutes on a low heat, stirring occasionally.
Crumbled bacon, cooked andoulle sausage and clams are the last ingredients to be added, and then simmered for 20 minutes more.
Once the soup is ladled into bowls, sprinkle black pepper, and place some fresh Thyme leaves on top as a garnish.