the jenova you see in neibelheim is the same jenova that's in the shinra building, just 5 years before that's all. this is also the same jenova that u hav to fight four times (as sephirtoh took jenova from the shinra building.

timeline: jenova is kept at neibelheim----->5 years later----->jenova is kept at shinra building----->not long afterwards----->sephiroth takes jenova from shinra building to go with him (to the promised land i suppose, tho his version of the promised land is a massive injury to the planet! :O)

btw, i hope the visual timeline helped!

sephirtoh's real mother is lucrecia, not jenova. however, lucrecia and sephiroth were injected with jenova cells while sephiroth was in lucrecia womb (sephiroth's father is hojo btw). I think this is why sephiroth regards jenova to be his mother, as he has inherited her DNA as well.

jenova is the "calamity from the skies" (everything about this topic is explained in the videos at icicle inn). and credit goes to russielloyd for mentioning jenova's virus turning cetra into monsters. jenova's arrival also began the construction of the weapons to counte it however, she was defeated before they were used, that's why they were never released. they were designed to fight the virus infecting the planet, and when released they thought humans were the virus and so attacked them.

cloud is a normal human like everyone else, born just like evryone else. hojo classes him as a failed experiment not because he created him but becuase of the experiments he ran on him after the neibelheim incident 5 years ago. see necro arc entry no.14 for info on why zack survived the expriments and cloud didn't.

i think that covers everything. gimme a shout if ur still confused!