Bring water to a boil in a large stockpot. Add fusilli; return to a boil. Cook, uncovered, 10 minutes or until fusilli is al dente, stirring occasionally. Drain.
Heat the olive oil in a large skillet over medium-low heat. Add the shallots, fennel seeds, and saffron (if desired). Cover and cook for 4 minutes or until shallots are tender, stirring occasionally. Stir in salt and tomatoes. Increase heat to medium; cover and cook for 5 minutes. Add the clams. Increase heat to high; cover and cook for 6 minutes or until clams open. Add shrimp, rind, and jalapeño. Stir gently. Cover and cook for 3 minutes or until the shrimp are done. Discard any unopened clamshells. Stir in fusilli.