Begin by prepping all ingredients. First, rinse off the clams as best as you can. Then, fill a large bowl with cold water and about ¼ cup or so of kosher salt. Mix, then add clams, ensuring all clams are covered by water. Place bowl in fridge for about 30 minutes while prepping other ingredients.
Finely mince all cloves of garlic, zest and juice lemons, and do any other necessary prep.
After 30 minutes the bowl of clams and water should have some dirt or sand in it. Drain the clams and rinse thoroughly.
Bring a large pot of water to a rolling boil. Salt the water with about 1 tablespoon of kosher salt. Cook linguine until al dente according to package directions. Drain pasta and reserve about a cup of pasta water.
Add saffron threads to a small bowl, then pour about ¼ cup of hot pasta water over threads and allow to steep.
In a deep skillet or pan, heat olive oil over medium low heat. Add minced garlic and stir gently until garlic is fragrant and soft. Avoid browning or burning garlic. Add red pepper flakes and lemon zest, stir.
Gently add the cleaned clams to the sauce. Arrange them in a single layer and then add the wine to the pan off of the heat. Return to the stove and cover pot. Steam for a couple of minutes, until all clams have opened up. If there are any unopened clams after about 5 minutes, discard those.
Once all clams are opened, use a pasta spider or a spatula to remove clams and place in a clean bowl. Carefully take clams out of the shells for about ¾ of the clams. Place un-shelled clams in a separate bowl.
Let the sauce continue simmering on medium high heat until it reduces by about ¼. Add the unshelled clams back to the simmering clam sauce. Add the saffron water, including the threads, to the sauce. Whisk in cold butter in cubes until emulsified and slightly creamy.
Add the cooked pasta to the pan of clam sauce. Gently toss to combine until the pasta is fully coated. If needed, add some of the pasta cooking water to thin the sauce. This may not be necessary.
Squeeze a bit of lemon juice to the pasta and toss to combine. Taste and season with salt and pepper as needed.
Plate the hot pasta in a bowl, then garnish with the clams that remain in the shells. Add about 4-6 clam shells per pasta dish.
Garnish with finely chopped chives or fresh parsley and another squeeze of lemon if desired.