Cook bacon in a heavy large pot over medium heat until fat renders, about 5 minutes. Add onions and shallots and saute until tender, about 8 minutes. Chop tomatoes in a food processor. Add to pot with clam juice, wine, bay leaves and dried red pepper. Simmer 20 minutes, stirring occasionally. Add potatoes to stew and simmer until tender, about 20 minutes. Season with salt and pepper. (Can be prepared 1 day ahead. Cover and refrigerate. Return to simmer before continuing.) Add clams to stew. Cover and simmer until clams begin to open, about 5 minutes. Add scallops and shrimp, cover and simmer until clams open and scallops and shrimp are cooked through, about 3 minutes. Discard and clams that do not open. Mix in half of basil. Transfer stew to a large serving bowl. Sprinkle with remaining basil and lemon peel.