I meant to comment on this earlier today, but the browser went crash and I got caught up by other things instead. However, better late than never.
So, wow!
I love the way you've described Cloud's struggle first to remain whole in the lifestream, and then to even *remain* under the twin onslaught of Sephiroth and Jenova. Zack's efforts to help him, and the way the last remnants of who Cloud is are fighting, because they can't tell the difference between friend and foe any more - it's so poignant, particularly the moment when Zack's personality almost overwhelms the last snippets of Cloud, to the point where Cloud becomes convinced he *is* Zack. The way the little snippets can't manage to string together sentences or thoughts, just feelings and emotions.
This story is so powerful, just the way you're showing things from the point of view of those the Sephiroth/Jenova matrix attempts to overwhelm. I found Malkhut interesting because the persona who became Kadaj realised he had power of his own, even as Sephiroth/Jenova tried to convince him he didn't. This one is beautiful because it shows their first attempt, in a way - and they've forgotten the important part about emptying a vessel, which is that punching a hole in the bottom is pretty counter-productive if you're planning to use the vessel again.