Fill a large bowl with cold water. Add a teaspoon sea salt and add the clams. Swish them around a little then let them soak one hour. Lift the clams out of the water, leaving any sand or grit that settled on the bottom of the bowl.
Set aside 1 cup of the tomatoes. Put the rest in a saucepan with the garlic, parsley leaves, chili, salt, saffron and 2 tablespoons olive oil. Add 4 cups water and bring to a boil. Reduce heat to a slow bubbling simmer and cook 30 minutes. Pour the broth through a strainer set over a bowl of small saucepan, (discard the vegetables).
Cook the fregola sarda in boiling salted water. In my experience it can take longer to cook than other types of small pasta before becoming tender, about 20 minutes. Drain and toss with 1 tablespoon of the olive oil cover and keep warm
Heat 2 tablespoons oil over medium heat in a saute pan large enough to hold all the clams (12 inches diameter should do it). Add the garlic and shallot and cook until fragrant and sizzling. Toss in the clams, reserved tomatoes, broth and lemon juice. Cover the pan and turn up the heat to high and cook until the clams open, about 5 minutes. Discard any clams that haven't opened. Taste the broth to see if it needs salt or chili.
Spoon the fregola into individual bowls and ladle with the clams and broth. Sprinkle with the chopped parsley.
Recipe inspired by Fish in Crazy Water in Marcella Cucina by Marcella Hazan