In a saucepan, heat milk and lemon zest over medium heat until steaming; remove from heat. In a bowl, whisk together until steaming; remove from heat in a bowl, whisk together 1/2 cup sugar and cornstarch, whisk in eggs. Gradually whisk hot milk mixture into egg mixture in a thin, steady stream.
Return to saucepan; cook over medium heat whisking constantly for about 8 minutes or until thickened to pudding consistency. Transfer to a clean, shallow bowl; stir in lemon juice and vanilla. Place plastic wrap directly on surface and let cool. Refrigerate until chilled, at least 3 hours or up to 2 days.
In a small skillet over medium heat, toast pecans, stirring constantly with a wooden spoon, for 4-7 minutes or until toasted and fragrant; transfer to a bowl and set aside. Quickly add remaining 2 tablespoons sugar and water to pan. cook stirring constantly until sugar is melted and starting to brown. Add 3/4 of the pecans back to the skillet; remove from heat and stir until pecans are glazed. Transfer to a baking sheet and spread in an single layer. Let cool. Finely chop the unglazed pecans; sprinkle in bottom of pie crust. Set glazed nuts aside.
Up to 8 hours before serving, spread chilled lemon filling in pie crust over chopped pecans, smoothing top. Cover and refrigerate. Just before serving, arrange glazed pecans, rounded side up, on top of filling.
COOKING TIP: Zest the lemons on a fine side of cheese grater or with a microplane-style grater. Then squeeze out the juice and refrigerate or freeze any extra in an airtight container for another use.
FOR THE ADVENTUROUS: Substitute Meyer lemons for the regular or add zest of 1 lime for a lemon-lime version. Top each serving with sweetened whipped cream.