Start with the onions and saute them in 3 tblsp olive oil on a medium heat till translucent, then add the fresh basil and turn down the heat while continuing to stir. Keep cooking the fresh basil to bring out the flavor, but still stirring the onions in the same pan. The basil leaves should be wilted and soft, but not burned. Then, add 3 oz of chicken stock and simmer till most of the liquid has burned off. Set aside.
Using a food mill (which can be purchased at specialty kitchen supply stores) separate the seeds and skin from the fresh tomatoes, then with a wooden spoon, stir in all of the dry spices. Then, stir in the onions, olive oil, stewed tomatoes, and fresh Basil mixture. You want to marinate all of this in the refrigerator for a couple of hours. The acids will be infused with the herbs the longer it sits in the refrigerator. Meanwhile, start in on the garlic.
Peel off the top layers from the garlic cloves and wrap each one in foil, place in a roasting pan. Roast the garlic under the broiler or a 425F oven for 20 minute Let cool and then unwrap. In a bowl, mash down the garlic with a fork, or potato masher, till it forms a paste, then in a blender with 1 cup of chicken stock, puree the roasted garlic paste till it liquifies. You are now ready to season the Marinara with garlic puree while it cooks.
Take the marinated tomatoes and seasonings from the refrigerator and place in a large stock pot or sauce pan. Simmer on a low heat, stirring and gradually adding the red wine vinegar, tomato juice, and remainder of the chicken stock, add in the garlic puree and keep simmering till it comes to a slight boil. After the first boil, is when you add in the flour depending on how thick you want the consistency to be. This Marinara usually simmers 45min to 1 hour, but you can also use a crock pot on low to keep it going longer, if desired. Stir in cracked black pepper to taste.