Kishi: That's very arrogant of you, saying it's pure fact. I'd like you to explain here how the "second Sephiroth" can ONLY be Jenova and not a clone.
The only thing that I see that supports your theory is that the Jenovas you fight as the game progresses.
However, there's still the matter of the "black-cloaked man" you're chasing. You follow him onto the boat to Costa del Sol...and the "second Sephiroth's" on the boat, but none of those disfigured clones. Shinra(the Turks, actually) trace him to the Temple of the Ancients, and there's none of those all-in-black guys there.
So, unless half the time you're chasing the "second Sephiroth" and half the time you picked up traces of just another clone, which seems highly unlikely and not mentioned at all in the game, the "second Sephiroth" cannot be Jenova-in-disguise.