Alright, before I run the calcs, the Defensive EVs were done in order to ensure a Vire OHKO and they happened to be 99% for Magnezone. I added 12 EVs I wasted to Satk and then recalculated a 100% OHKO rate. So here are the same calcs I did, but redone just to ensure accuracy. (crosses fingers)
An Empoleon with Torrent activated, holding Leftovers, and a Positive nature with 100 Sp.Atk EVs attacking (with Hydro Pump) a 172 HP Magnet Pull Magnezone holding Leftovers (31 IVs all around) takes... 86.73% - 102.16%. Goddamit, where did I mess up? I must have mixed up him and vire somewhere.
248 EVs (Hydro Pump) does 98.15% - 115.43% to it, with Hydro Cannon OHKOing. Dammit. I'm sorry, all the guys I yelled at.
Hydro Cannon with 100 Special Attack EVs does 108.33% - 127.47% to a Standard 'Zone, but leaves you vulnerable... much like Porygon-Z.
Where you went wrong with the zone calcs is that instead of using the standard 172 HP EV zone, you calculated it with a max SPATK and max SPD zone. With no HP EVs, the SPATK EVs you gave to empoleon would do exactly minimum 100% with torrent hydro pump. But since not many people actually use a no HP magnezone, that doesn't really help.

