Stir together 1 cup sugar and lemon juice in a 1 1/2-quart saucepan over medium heat, and cook, tilting pan to melt sugar evenly and stirring occasionally, until sugar melts and turns a light golden color. Stir in butter.
Whisk together remaining 1 cup sugar, egg yolks, milk, and flour in a heavy saucepan; bring just to a simmer over medium heat, whisking constantly.
Add sugar mixture to milk mixture immediately, and cook, whisking constantly, for 5 to 7 minutes or until it has a pudding-like thickness. Stir in pecans. Cover, placing plastic wrap directly on filling, and chill 8 hours.