I'm having a little trouble following you here. But if you're asking about how Sephiroth and Jenova share the same motives, you can think of it like this: Jenova was essentially a virus. Its goal was to infect and take over every living thing on the planet. Sephiroth hoped to do the same thing by injuring the planet and absorbing the lifestream. It's a little more complicated than that, but that's the gist of it.
Or was clearly and unapologetically stabbed through the stomach. According to the game, and everyone else but you. Here, look! Watch: http://dl.speeddemosarchive.com/FinalFantasy7_PC_741/FinalFantasy7_PC_741_part74.avi (100 meg Dl, sorry. 18:31 in) (Also, if you really like the game, that's it being beat in 7 hours and 41 minutes)
I dunno. To me, it looks pretty clearly like it's going through the right shoulder:
At worst, it's through the center of the chest, which isn't necessarily fatal given immediate medical treatment (which Cloud had). The state of medicine in FFVII's world isn't explained all that well, but it seems quite advanced. The healing effects of Mako and Jenova's cells are hinted at as well.
In any case, I think this is a pretty minor detail.
How exactly Cloud overpowered Sephiroth when everyone else failed is up for some debate. I tend to think this scene is telling us that Sephiroth was never the all-powerful god figure he was made out to be. He was ultimately just a man. There's also some suggestion that Jenova cells don't precisely make a soldier "stronger," but just enable him to resist death, as Lucretia says. (Obviously this ties back to how Cloud survived his stab wound if it really was to his chest and how Sephiroth survived his fall). Finally, you should look to the underlying meaning of the scene, which is that Cloud did have an immense inner strength after all, despite how weak he felt--it just wasn't the kind of strength that would get him into SOLDIER. It's an extremely powerful scene in any case.
Oh, and if you really want to get practical about it, keep in mind that Sephiroth had just been stabbed through the back with a foot-wide blade, something that would have already killed anyone else. Obviously he was weakened.
I... don't really follow you here. Is it that you don't believe Hojo came and picked up Cloud and the others from the reactor? Then it sounds like you missed this optional scene which covers some of those events. The remaining missing events are explained through dialogue with Hojo and from the documents you can read in various places: just after Sephiroth fell into the reactor, Hojo and some Shinra soldiers arrived at the scene. They rounded up all the survivors and enlisted them into the Jenova project. They then rebuilt the town to cover up what had happened. The Nibelheim survivors were injected with Jenova cells and tattooed, and became the "Sephiroth clones." (Again, they weren't literally clones of him).
Which completely explains why this guy is suddenly all powerful. He's been encased in ice from a fatal fall caused by someone entirely not powerful! Genius!
I don't know why you figure he's all-powerful. In person, Sephiroth doesn't really do anything all that amazing. Are you thinking of the final battle and all the crazy galaxy-destroying shit he does? Most of that didn't actually happen.
"The ability to change one's looks, voice, and words, is the power of Jenova."
Sephiroth, being half-Jenova, possesses that power of illusion. The ridiculously over-the-top events of the final battle are a strong hint about that.
Or if you're thinking of when he was flying around killing people on the cargo ship and elsewhere, remember that that wasn't Sephiroth himself. It was the various body parts of Jenova, which, largely as a result of his trip through the lifestream and the knowledge it gave him, Sephiroth had gained the power to control. Jenova had a lot of strange powers, but there's nothing too surprising about that. She was an alien monster-thingy.
No, those weren't physical/look-alike clones either. As I said above, the people in the black capes were the citizens of Nibelheim, twisted by the Jenova project. Sephiroth could control them to a certain extent (just as he controlled Cloud) because they had Jenova cells in their bodies. But the "Sephiroths" who were actually running around in his form massacring things were Jenova body parts manipulated to resemble Sephiroth, not the "clones." The "clones" didn't do much more than stagger around moaning on their way to the northern crater, and poke around for the black materia a bit.
As for why they were cut up when they reached the crater, it was to complete the "Jenova Reunion." They had to be killed so that Sephiroth could retrieve the Jenova cells within them and reconstruct his body.
I don't see your problem with this. If whatshisname-the-martial-arts-guy could only carry out one person, why is it hard to believe he would choose his dearest student? And Hojo didn't ignore Tifa -- she was rescued before he got there.
Also, so Cloud's not a clone, he's... a regular guy, who mysteriously "Kills" the most powerful guy in the world, survives a wound to the stomach that kills Aeris, then coincidentally gets kidnapped and survives a make treatment that makes others worthless and immobile.
It wasn't a coincidence that he was kidnapped. Shinra had to round up and silence every witness to cover up what Sephiroth (and they) had done, and putting them in the Jenova project was the obvious thing to do.
And the treatment did make Cloud worthless and immobile -- that's what the scene you mentioned of him "dying in Midgar" was all about. He wasn't dying -- he was suffering from severe Mako poisoning and disorientation as a result of what happened to him. He recovered because Tifa found him and he was able to latch onto her memory and the memory of Zack, and reconstruct a personality for himself. But the new personality was unstable and full of holes, which is why he was so screwed up for most of the game.
FFVII's story is remarkably well put-together and internally consistent. I'm more impressed with it every time I look at it.
