Fill a large pot or Dutch oven halfway with water and bring it to a boil. Working in batches, add tomatoes and boil for 1 to 2 minutes, or until the skins begin to split.
Remove the tomatoes with a slotted spoon and place them in an ice water bath. Peel and quarter the tomatoes over a large bowl so you save the juices. Remove the tough stem area. The tomatoes do not need to be seeded.
In a food processor, pulse the onions and bell peppers in batches until finely chopped. For extra flavor, you can sauté the peppers and onions in a little oil with a pinch of salt before adding them to the sauce.
In a large stockpot, combine the tomatoes, onion and pepper mixture, tomato paste, soy sauce, Worcestershire sauce, brown sugar, salt, garlic, oregano, basil, red pepper flakes, and bay leaves.
Bring to a boil. Reduce heat and simmer uncovered for 4 to 5 hours, stirring every 15 minutes or so to prevent scorching. Remove and discard the bay leaves. For a smoother sauce, use an immersion blender to blend until smooth.
Add 2 tablespoons bottled lemon juice to each hot quart jar, or 1 tablespoon bottled lemon juice to each hot pint jar. Ladle hot sauce into hot jars, leaving 1/2 inch headspace. Remove air bubbles, wipe rims clean, and add lids and rings.Do not forget the lemon juice! If you forget to add the lemon juice you will need to open the jars, add the juice, replace with new lids, and reprocess.