Cook and stir salt pork in a 5-quart Dutch oven or heavy kettle over medium-low heat until crisp, 10 to 15 minutes. Add onion, leeks, and garlic to salt pork; cook and stir until tender, about 5 minutes.
Mix clam juice, potatoes, boiling water, green bell pepper, carrot, and celery into salt pork mixture; cover Dutch oven and bring liquid to a boil.
Separate necks from soft parts of each clam. Coarsely chop necks and add to salt pork-vegetable mixture, reserving soft parts. Reduce heat to medium-low and simmer salt pork-vegetable mixture until potatoes are tender, about 20 minutes.
Stir soft parts of clams, tomatoes, ketchup, parsley, salt, thyme leaves, black pepper, and bay leaf into salt pork-vegetable mixture; bring soup to a simmer.
Melt butter in a small saucepan over medium-low heat; stir in flour until smooth. Spoon about 1 tablespoon liquid from soup into butter-flour mixture and stir until smooth; add to soup and stir. Cover and simmer soup until thickened, 15 to 20 minutes.