Using a large slotted spoon, transfer shells to a colander. Rinse with cold water; drain well and set aside. In same pan cook tiny shells according to package directions. Drain; set aside.
Meanwhile, in a large saucepan combine Gruyere cheese, cheddar cheese, half-and-half and pepper. Heat over medium-low heat until cheese is melted and smooth, stirring frequently. Once melted, stir in sausage, garlic, and shallots. Stir in tiny shells.