Bring water to boil for pasta. Preheat oven to 350°F.
Cook pasta al dente, according to package directions. Reserve 1/2 cup pasta water; drain pasta. Set aside.
In bowl, mix crab, cheeses, soy sauce, milk, scallions, jalapeños and chile flakes. Stir well; add reserved pasta water to cheese mixture and stir well. Add pasta to cheese mixture. Stir. Place in 1-quart baking dish or individual 8-ounce ramekins. Bake 25-30 minutes until bubbly and creamy.
While pasta is baking, cut wontons into triangles. Heat oil in skillet and fry wonton pieces in batches until crisp. Drain and season with salt to taste.
Serve pasta with crispy wonton wrappers on the side.