In a saucepan of boiling water blanch tomatoes, 2 or 3 at a time, 10 seconds and transfer to a bowl of ice and cold water. Peel, seed, and dice tomatoes.
In a large heavy kettle steam clams in water, covered, over moderately high heat 5 to 10 minutes, checking after 5 minutes and transferring them as they open to a bowl. (Discard any clams that are unopened after 10 minutes.) Remove kettle from heat. Strain liquid into a small bowl leaving any sand particles behind. Rinse pot and return strained liquid back into the pot.
In a 6 quart kettle bring 4 quarts salted water to a boil and cook linguine until al dente. Drain linguine in a colander.
While linguine is cooking, with a small knife remove meat from the largest 24 clams, discarding shells, and in a food processor pulse just until chopped coarse. Into reserved clam liquid stir chopped clams, tomatoes, garlic, oil, and red pepper flakes and simmer 2 minutes. Add linguine, basil, remaining 12 clams in their shells, and any liquid in bowl and toss well with salt and pepper to taste