Place the clams and water in a large frying pan over medium high heat. Cover the pan and cook until the shells open, 4 to 5 minutes. Remove the clams with a slotted spoon and place in a bowl. Let the clams cool 5 minutes. Discard any clams that do not open. Shuck all but 10 clams and reserve. Discard the shells.
In a large frying pan over medium heat, warm the olive oil and add the garlic. Cook, stirring often, until the garlic is light golden, 1 minute. Add the fregola to the pan and stir to coat the grains well with the olive oil, 1 minute. Add the tomatoes, crushed red pepper flakes, 2 tablespoons of the parsley, chicken stock and reserved clam juice. Stir together. Simmer slowly until the fregola is double in size and firm to the bite but cooked through, 20 to 25 minutes.
Just before serving, add the clams and stir together. Season with salt and pepper. Transfer the fregola to a deep serving platter. Garnish with the reserved clams and sprinkle the remaining 1 tablespoon parsley on top. Serve immediately.