Set a large 1-gallon pot of water with a pasta insert over high heat. Bring to a boil and add 2 tablespoons salt.
Add the uncooked pasta to the water and cook for 7 minutes. (The pasta should be undercooked.) Drain the pasta in a colander and reserve.
Begin making the sauce while the pasta is cooking. Set a large 14-inch saute pan over medium-high heat. Add the olive oil to the pan and once hot, add the onions and saute until lightly caramelized and translucent, about 3 minutes. Add the garlic and crushed red pepper flakes, and saute until fragrant, about 30 seconds.
Add the wine and tomato paste, stir to combine well, and cook until the wine has nearly completely evaporated, about 3 minutes.
Add the diced tomatoes, remaining teaspoon of salt, and the par-cooked pasta to the pan, toss to combine, and bring the sauce to a boil.
Add the clams to the pan and cover. Continue to cook until the shells open, 5 to 7 minutes. Add the parsley and toss to combine. Drizzle the extra-virgin olive oil over the pasta and toss to combine.