Preheat the oven to 350 degrees F.
In a heavy 2-quart saucepan, bring the water to a boil. In a small bowl, combine the flour and sugar, tossing with a fork to blend. Add the flour-sugar mixture to boiling water and cook, whisking often, until thickened, about 6 minutes. Remove from heat and slowly add the eggs, whisking vigorously. Return to medium-low heat and cook, whisking, until velvety smooth, about 3 minutes. Add the vinegar and lemon extract and whisk just to blend.
Pour into the cooled pastry shell and refrigerate until set, about 3 hours.
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