Chicken Marinade: In a large, shallow glass baking dish, mix together soy sauce, ¾ teaspoon dried thyme, ¼ teaspoon cayenne pepper, ½ teaspoon paprika, 5/8 chopped onions and ½ teaspoon black pepper. Place the chicken in the marinade. Refrigerate for at least 3 hours.
While chicken is cooking, saute bacon in a Dutch oven (or large skillet) over medium heat until brown. Add the onion and garlic. Continue to cook 5 minutes. Mix in flour and sausage. Cook 5 minutes more; stirring frequently. Add the ham, thyme, cayenne, chicken stock, tomatoes, reserved juice and green peppers and bring to boil. Cook for 25 minutes.
Add cooked chicken to jambalaya.
Just before serving the jambalaya, add the shrimp and cook for 3 minutes until they are firm to the touch.
Serve over steamed rice.