Preheat oven to 350 degrees. In a large bowl, whisk together 3 1/2 cups flour, wheat germ, confectioners' sugar, and 1/2 teaspoon salt. Using a pastry blender, cut in butter until largest pieces are size of peas.
Press mixture into bottom and up sides of an ungreased 17 1/2-by-12 1/2-inch rimmed baking pan. Bake until golden, 20 to 30 minutes. Transfer to a wire rack to cool.
In a medium bowl, whisk together eggs, granulated sugar, and remaining 2/3 cup flour until combined. Whisk in lemon and lime juices, zests, and remaining 1 teaspoon salt until combined. Pour filling onto crust.
Bake, rotating pan halfway through, until center is set, about 30 minutes. Transfer to a wire rack to cool completely. Dust with confectioners' sugar, and cut into bars approximately 3 by 2 inches. Bars can be stored at room temperature for up to 1 day, then kept in an airtight container in the refrigerator for up to 3 days.