Hmm....
Could Cloud be part of the experiment which created Sephiroth (just donated DNA, not involved) and then enter the RoD which corrupted Sephiroth? (Sorry, I looked back over your original post and noticed an issue with Experiment Sephiroth vs RoD Sephiroth)
I don't have a good answer for you in regards to traveling the worlds, sorry.
It's ok, you're still helping me out a lot with the little kinks, so I'm really grateful. =)
Cloud being part of the experiment which created Sephiroth would have meant that Even would have had to outright find a way to take DNA from him since Cloud is a member of Radiant Garden. That probably wouldn't have sat well with Ansem at all, and could be a step towards the rift between Ansem and his apprentices. Is there any mention of Ansem's apprentices experimenting on the hearts of people that weren't themselves? Because if there is, Cloud could have been a victim of that.
And then the traveling of the worlds...perhaps Zack could have gone to Radiant Garden and been one of the people that escaped on Cid's ship. Cloud would have been among them. Cloud bonds with Zack, Cloud is interested in getting stronger so he can take back Radiant Garden. I imagine that would be a very common feeling among people in Traverse Town - the idea that they should just get stronger so they can take down the darkness and restore their world. Cloud however, feels he can't do it in Traverse Town. So Zack asks Cid to build them a smaller ship, and teach them how to pilot it. Zack and Cloud go to Olympic Coliseum, where Zack helps Cloud train and the two stay there for a number of years.
Then Cloud meets Sephiroth in battle. Sephiroth senses a DNA link between them, and takes an interest in Cloud.
Meanwhile, some sort of event happens where Sephiroth torches Thebes, and Cloud gets a moment of recklessness and follows Sephiroth right into the RoD. Worried about what's going to happen to Cloud, Zack doesn't think twice, and follows him in. Maybe the Organization wants Even, now Vexen, to go and get his old creation back?
A second option built from that could be that Vexen goes to the Coliseum to get Sephiroth and he can't. So he takes Cloud instead. Zack goes to save Cloud. Vexen could have taken cloud to lure Sephiroth back to him. Sephiroth knows its a trap, but wants to destroy the nobody of his creator anyway, so he goes after him. But that all depends on how much Vexen remembers of his past life. I think it's probable that he could remember creating Sephiroth in his past life, since Days indicated that Xigbar knows
a lot more about Xemnas than anyone else, stemming from his experiences as his somebody in BBS.
Then it could just be indicated that Angeal is part of Olympic Coliseum as well, and Zack got the buster sword from him.
Do you think this will work? And I'll definitely take a look at your fic, it sounds really interesting.