Preheat the oven to 350 degrees F with a baking sheet on the middle rack.
Roll out the pie dough on a lightly floured surface with a lightly floured rolling pin into a 12-inch round. Fit into a 9-inch pie plate and trim the edge, leaving 1/2-inch overhang. Fold the overhang under and lightly press against rim of pie plate, then crimp decoratively. Lightly prick the bottom all over with a fork. Chill until firm, at least 30 minutes (or freeze for 15 minutes).
Meanwhile, melt the butter in a small, heavy saucepan over medium heat. Add the brown sugar, whisking until smooth. Remove from the heat and whisk in the vanilla, zest, salt, and agave nectar. Lightly beat the eggs in a medium bowl, then whisk in the butter and brown sugar mixture.
Put the pecans in the pie shell and pour the butter and brown sugar mixture evenly over them. Place on the hot baking sheet and bake until the filling is set, 50 minutes to 1 hour. Cool for 1 hour before slicing and serving.
Blend the flour, sugar, and salt in a food processor. Add the butter and shortening; pulse until the mixture resembles coarse meal. Drizzle 4 tablespoons ice water over the mixture. Process just until moist clumps form, adding more ice water by teaspoonfuls if dough is dry. Gather the dough into a ball and flatten into disk. Wrap in plastic. Chill 1 hour.