Submerge your fresh clams in some cold water 20 minutes prior to cooking. This helps release any sand there may be inside. Then scrub them individually and rinse.
Bring a large pot of water to a boil and add the 1 tablespoon salt and the linguine. Cook until just shy of al dente (will cook for a few minutes in the sauce). Reserve 1/2 cup of the pasta water for the sauce later.
In an extra large deep skillet, heat your oil and add the shallots and saute for a minute or two. Stir in the garlic for 15 seconds. Add the wine, chili pepper flakes, salt to taste, canned clams, 1/4 cup parsley and fresh clams. Bring to simmer and cover and cook until the clams open - about 6 to 8 minutes. Discard any unopened clams.
Remove the clams from the pan and cover them to keep warm. Add the cooked linguine into the pan and toss it around for a few minutes to coat with sauce. Add the reserved pasta water to help the sauce stick to the pasta.
Remove the pan from the burner and add in the butter, lemon juice and remaining parsley and toss until butter is melted. Taste and adjust salt if necessary. Add the clams back in the pan to serve or just add them on top of each plated serving.
Notes
You can leave out the fresh clams and the sauce will be great with only the the canned. Conversely you can also omit the cans and just use the fresh.