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.