In a large, heavy-bottomed pot, bring about an inch of salted water to a boil. Gently place 4 dozen of the 5 dozen clams into the pot, cover and let steam until the clams have opened, about 5 minutes. Check them frequently, move them around with tongs or a long- handled spoon as needed and remove the clams to a large bowl as they open so that they do not become overcooked and rubbery. Do not discard the cooking liquid.
As soon as the clams are cool enough to handle, remove them from the shell with a soup spoon or clean fingers, keeping them intact as much as possible, and collecting as much of the liquor from within the shell as possible. If they’re a little on the large side, give the clams a rough chop. Strain the cooking liquid through a fine-mesh sieve into a small bowl.
Wash out the pot, fill it 3/4 full with heavily salted water and bring it to a boil.
When the water is just about to boil, warm the oil in a large, heavy-bottomed sauté pan and add the garlic and pepper flakes. Cook over medium-low heat, taking care not to let the garlic get brown, which can happen in an instant. Add the wine and increase the heat so that the wine boils and reduces by half. Add the reserved clam liquor and a good splash of the clam cooking liquid, then the remaining 1 dozen clams. Cover and cook until the clams have steamed open. Remove the clams to the side as they open, and discard any that haven’t opened within a reasonable amount of time. (It’s not terribly uncommon to have 1 or 2 clams per dozen that just never open.)
Add the linguine to the boiling water and cook according to the package instructions until just al dente.
While the pasta cooks, add the reserved cooked clams to the sauté pan and season with salt and pepper to taste. Add the butter and toss over the heat until everything is just hot.
Place a colander over a mixing bowl or clean pot, so that you may capture some of the pasta cooking water, and drain the cooked pasta in the colander. Immediately add the pasta to the pan with the sauce. Toss over the heat for 1 minute, adding some of the reserved pasta water, 1/4 to 1/2 cup at a time, if necessary, to loosen up the sauce. Garnish with the parsley, then transfer to a serving bowl. Add the clams in their shells and serve at once.