Position a rack in the center of the oven and heat the oven to 325°F. Season the cod with salt and pepper. Let it sit at room temperature while you prepare the braising mixture.
Heat the olive oil in a 12-inch ovenproof skillet over medium-high heat. Add the fennel, sprinkle with a pinch of salt and pepper and brown on both sides, about 5 minutes total. Remove the pan from the heat and transfer the fennel to a plate. Put the pan over low heat and add the garlic, shallot, 1/2 tsp. salt, and 1/4 tsp. pepper. Cook, stirring, until just softened, 1 to 2 minutes.
Add the clam juice, potatoes, tomato, liqueur, bay leaf, thyme, fennel seed, and saffron to the skillet. Raise the heat to medium and bring to a simmer. Simmer for 3 minutes to start the potatoes cooking. Nestle the cod pieces and clams into the sauce, piling the fennel on top of the fish and making sure all of the potatoes are submerged. Tightly cover the pan with a lid or aluminum foil and braise in the oven until the fish is almost cooked through, 10 to 15 minutes, depending on thickness.
With a slotted spatula, transfer the cod to 4 shallow bowls. Bring the braising liquid, clams, and vegetables to a brisk simmer on top of the stove, cover the pan, and cook until the clams are opened and the vegetables are tender, 3 to 6 minutes more. Divide the opened clams (discard any unopened ones) and vegetables among the bowls. Add the fennel fronds and parsley to the braising liquid in the pan. Bring to a simmer and pour over the fish and vegetables.
Crusty garlic bread served alongside is perfect for soaking up the flavorful sauce.