Ahh, ok, that explains why when I opened with Shiva, Jenova didn't even get her spawns out before she went down! The other stuff I had kinda figured out, but I wasn't 100% sure if it worked like that!
Non game-play question: When the party reaches Coasta Del Sol, there's a cutscene where Rufus and Hediegyahaha are supposed to leave the boat, and Rufus gets on a helicopter. But in the mod, they both get off the helicopter (?) and then Rufus gets back on. Is there a reason this was changed (other than Heidegyahaha being in position to toss the Shinra Manager off screen XD)?
And possible bug: When first visiting the Gold Saucer, if you go to the roller coaster ride where you meet Dio for the first time, the "chase" music plays instead of the normal GS theme. I know the music plays there when you're chasing Cait Sith around later on, but maybe look into that?
And finally, part of my previous issue was that I wasn't using the level-up sources! Like, I would see "Check SP" when at a save point, but I didn't know how to spend the points. I thought I had to back-track to the cave, but when that didn't do anything, I had to double-check the documentation which DOES say there's an option in the Save-Point interface, but I never saw it. It was THERE, i just... never looked UP >_< Perhaps as a possible QoL thing, have the option to "Spend SP" underneath "Check SP"? Also, when I did that, it did Cait 3 times, is that normal?