In a large bowl or baking dish combine tomatoes, onions, and vinegar and season with pepper and salt. Marinate mixture, covered, tossing occasionally with a rubber spatula, 30 minutes. Transfer tomatoes and onion to a plate with a slotted spoon and add arugula to marinade remaining in bowl or baking dish. Season arugula with pepper and salt and toss. Arrange arugula on bottom focaccia half and top with mozzarella, tomatoes, onion, and remaining focaccia half, pressing together gently.