In 2-quart glass batter bowl, whisk together the sugar, flour, and salt.
In a separate bowl, combine milk, evaporated milk, and water.
Add half of milk mixture to the flour and sugar mixture; mix smooth. Microwave one minute at a time on full power, until smoothly thickened, whisking after each minute. This takes approximately 5 minutes total.
Add eggs to remaining milk mixture and whisk. Gradually whisking into the hot mixture so eggs don't curdle.
Continue microwaving one minute at a time, whisking after each minute, until thick and smooth. (As it gets thicker, you may want to stir after each 30 seconds or reduce power.) This takes approximately 5-6 minutes total.
Whisk in butter, chocolate chips, and vanilla, stirring until chocolate is completely melted and smooth.
Pour into baked pie shells. Cover with plastic wrap. Chill.