It's been a while since I posted in this thread, so...

This Sephy, who was induced by Jenova Cells, was badly hurt by Zack.
Cloud was the one who threw him into the Lifestream, not Zack. The real Sephiroth is frozen in a Mako Crystal in the Northern Crater.

Hojo continues the experiment, attempting to make clones of Sephiroth using the cells from the organism found 2000 years ago. Cloud is one of them, but bears no mark as he's a failure.
Hojo only conducted experiments on Cloud. Cloud really did exist, he wasn't an actual clone, although the records seem to say he is.

Zack disappears ot gets shot or something, and Tifa's memories of Zack become Cloud's identity.
(She doesn't want to let go of her love for Zack. She's as messed up as everyone else.)
Aeris was the one whom loved Zack. Tifa only went along with Cloud's story. It would have been a little messed up if Tifa were to claim that Cloud's story (at Kalm) was a lie. That's why whenever Cloud paused, you saw a little "..." above Tifa.


And this may be WAY off topic, but at Wallmarket, when you can chose between 3 medicines, do any of them have an effect on the clone in Sector 5?