Heat 3 tablespoons oil in a large pot over medium heat. Add onion and fennel; sauté 5 minutes or until tender. Add minced garlic, thyme, and red pepper; sauté 1 minute. Stir in tomato paste; cook 1 minute. Add wine, cook on high 5 minutes or until reduced by half. Add tomatoes with juices, clam juice, water, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Boil; reduce heat to low, and simmer, partially covered, 10 minutes.
Preheat oven to 300°. Raise heat on stove to medium; add clams. Cover; cook 5–8 minutes or until shells are just opened. Remove clams (discard unopened shells). Set aside; keep warm. Lower heat to simmer. Season halibut with remaining 1/4 teaspoon salt and 1/4 teaspoon pepper; add to pot with basil. Cover; cook 2 minutes. Turn off heat, and stir in shrimp and scallops; cover. Let sit 6–8 minutes or until shrimp and scallops are just cooked. Return clams to pot; cover.
Arrange bread on a baking sheet. Drizzle with remaining 1–2 tablespoons oil; bake 12–15 minutes or until golden. Rub smashed garlic onto each slice.