Make the crust: Combine flour, sugar, and salt in a food processor. Add butter. Pulse to a coarse meal consistency.
In a small bowl, stir the vinegar and water together. Add to the processor slowly, pulsing, until a dough forms.
Form dough into two equal balls and flatten into disks. Wrap each disk in plastic wrap and chill overnight.
On a lightly floured surface, roll out 1 dough disk to a 12-in. circle (save second disk for another use). Mold into a 9-in. pie pan and flute the edges. Freeze.
Preheat oven to 375° and remove pie crust from freezer. Place a coffee filter in the crust, fill with dried beans, and partially bake until lightly golden, about 20 minutes. Let crust cool.
Make the ganache: Put chocolate in a medium metal bowl and set over (not in) a pot of simmering water and melt chocolate half way. Remove bowl from pan.
In a pot, bring cream and corn syrup to a soft boil, then pour over chocolate. Stir mixture together, then blend with an immersion blender. Add bourbon and butter. Blend again to emulsify. Pour mixture into the cooled crust. Chill for 30 minutes.
Preheat oven to 350°. Make the filling: Melt honey and butter in a pan. Let cool.
In a bowl, mix eggs, brown sugar, salt, and zest with a hand blender. Emulsify honey and butter into the mixture. Blend in flour, then add juice, vanilla, and bourbon. Strain.
Sprinkle walnuts over ganache, then pour filling over walnuts.
Bake until pie is set, nuts are toasted, and filling begins to crack at edges, 45 to 55 minutes. Let cool for a minimum of 4 hours before cutting.