In a large saucepan, combine sugar, flour, and lemon rind. Mix well, then whisk in vinegar and water. Cook mixture over medium heat, stirring constantly, until it comes to a boil. Continue to boil and stir for 1 minute. Remove from heat.
Place eggs in a medium bowl. Slowly whisk 1/2 cup of sugar mixture into eggs. Whisk egg mixture back into remaining sugar mixture. Stir in butter or margarine. Pour mixture into pastry shell.
Bake in preheated oven for 10 minutes. Reduce heat and bake 30 minutes more. Filling will still be liquidy but will firm as pie cools. Cool completely before serving.