Okay, it's a bit confusing but here it goes.

Clone deal - By clone they mean Jenova+Mako enhanced, not the sheep sort. Most especially because, if Cloud was a clone in that sense, he would have looked exactly like Sephiroth. Clone was actually a pretty poor word. What happened was, Cloud and Zach were taken and put in the tubes in the basement of Shin Ra mansion (this is a cut scene you may have missed, go down and examine the tubes if you havent already). Cloud wasnt killed, just wounded.

Tifa's memories... well, Tifa is handling Cloud with kid gloves throughout the game. She senses something is up, but she doesnt know what, and she doesnt come right out and say that she knows Cloud's memories arent right. Instead she gently steers him in the right direction... it's very possible that if she had come right out and corrected him, he would have either denied it or lost his mind. What Cloud should and shouldnt know, he probably makes it up as he goes along (that voice in his head helps) and he probably talked a lot with Zach, so he got the basics on that guy. Obviously he didnt know everything Zach knew (or else he would have known Aerith).

And if I'm right in remembering (it's been a while) isnt it Sephy that gets stabbed in the chest, not Cloud?