Bring a large pot of water to a boil over high heat, and add a handful of salt. Drop the pasta into the boiling water and stir to keep it from clumping together and cook until al dente. Drain and set aside.
Heat a large heavy skillet over medium-low heat, add the pancetta and cook until crispy, about 10 minutes. Remove the pancetta from the pan and drain on a paper towel. Drain fat from pan.
Add 3 tablespoons olive oil to pan over medium heat, add garlic, shallots, red pepper flakes and cook for 1 minute. Then add clams, white wine, tomato sauce and thyme to the pan and cook, covered, for 3 to 5 minutes or until clams have opened. Season the shrimp, calamari, and the scallops with salt and pepper and raise the heat to medium-high. Add the seafood and cook until the shrimp just starts to turn pink and the squid and scallops become opaque, 2 to 3 minutes.
Add the pasta into the pan and toss until coated with the sauce. Transfer the pasta and shell fish to a large serving platter and garnish with the basil, parsley, pancetta, and coarsely ground black pepper. Drizzle with extra-virgin olive oil and serve immediately.