Bring a large pot of lightly salted water to a boil. Add pasta and cook for 8 to 10 minutes or until al dente; drain.
Preheat oven to 450 degrees F (230 degrees C).
Melt butter in a large heavy skillet. Add red pepper, zucchini, garlic, and shallots. Saute over high heat until the shallots begin to soften; about 4 minutes. Mix in capers, salt and pepper. Remove from heat and add clams and shrimp. Toss until it's fully mixed.
Transfer mixture to a large baking dish. Cover and bake in a preheated oven until the clams have all opened and shrimp is cooked. Make sure the lid is not touching the shrimp or they'll burn and stick. Cook about 20 to 25 minutes, stirring occasionally.
Pour the scampi over the linguine, top with fresh basil and serve.