Put shells, 3 cups water, and salt in 5-quart Dutch oven. Boil, then steadily simmer uncovered 10 to 12 minutes, stirring frequently to prevent sticking.
Add reserved water in 2-tablespoon increments if drying before shells nearly tender. Leave about 1/4 cup starchy liquid; do not drain.
Add evaporated milk; gently simmer 2 to 3 minutes until shells tender and lightly coated.
Remove from heat. Stir in American cheese, cheddar in 3 additions, then mustard and pepper until smooth.
Rest 2 minutes; stir again. Loosen with unused measured water a tablespoon at a time if needed; serve immediately in 4 bowls.