Fill a large pot or Dutch oven half-way with water, bring to a boil. Using a slotted spoon, add tomatoes one at a time until you can't fit any more (about 8-10 tomatoes).
Boil for 1-2 minutes. Remove tomatoes one at a time with slotted spoon and plunge in an icewater bath. Peel and quarter tomatoes.
In a food processor, cover and process green peppers and onions in batches until finely chopped (if you want to add extra flavor, saute the peppers and onions in a little oil and a pinch of salt before processing).In a large stockpot, combine the tomatoes (do not discard excess juices from the tomatoes), onion/pepper mixture, tomato paste, soy sauce, Worcestershire sauce, brown sugar, salt, garlic, oregano, basil, pepper flakes, and bay leaves.
Bring to a boil. Reduce heat; simmer, uncovered, for 4-5 hours, stirring every 15 minutes or so (tomatoes burn easily so keep an eye on it). Discard bay leaves.If you want to make your sauce thick and smooth, use an immersion blender to blend the tomatoes until smooth with no large chunks (you can also blend it in batches in a blender).
Add 2 tablespoons lemon juice to 9 or 10 hot 1-quart jars (depending on how much sauce you have). Ladle hot mixture into jars, leaving 1/2-in. headspace at the top. Remove air bubbles; wipe rims and adjust lids.
For Water Bath Canning:
Process for 40 minutes in a boiling-water canner for altitudes of 1,000 feet or less. For altitudes up to 3,000 feet, add 5 minutes; 6,000 feet, add 10 minutes; 8,000 feet, add 15 minutes; 10,000 feet, add 20 minutes.
For Pressure Canning:
Using a weighted-gauge pressure canner, process 20 minutes for pint jars and 25 minutes for quart jars. Process at 10 lb for altitudes between 0-1,000 feet. Process at 15 lb for altitudes above 1,000 feet.