so then why does it go back further in the final battle with no dire consequence to anyone around him?
It does. It explodes in Viktor's face.
How was Victor the mage that gave Jace the rune that set him on this path?
Time travel shenanigans.
Ekko hitting him upside the head is what made Victor stop long enough to reconsider
Getting hit upside the head gave him pause, which gave Jayce the opportunity to speak to Viktor. Jayce's words are what made him reconsider.
Piltover harbor? How?
What do you mean, "how?" Did you think the orb was immobile, or do you just not understand how logistics work?
How did Orianna-bot come into being?
We literally see Singed take Viktor's Arcane juice from the orb using the same syringe we saw him adding shimmer into Ori's casket, and throughout the season we see that he plainly understands how the evolution seems to work. It isn't difficult to extrapolate that he simply replicated the process in a controlled environment.
How can she continue to exist post-Victor?
The same way Warwick does. The two of them -Warwick and Orianna- aren't simply Evolved like the dolls Viktor made. They're both a synthesis of hextech, chemtech, and Arcane. The difference is that Orianna was never directly augmented by Viktor, and never had her mind subsumed. She was never bound to him.
"No, you won't."
Sky wasn't "real." She was a representation of Viktor's humanity and emotion. His Jiminy Cricket, if you will. When he gave up his humanity for Evolution, that part of him died and she vanished.
I also really don't understand the transition
He saw that simply trying to be "good" didn't work and realized that the source of humanity's virtues -our emotions- were also the source of our evils. Therefore, he endeavored to remove emotion, not understanding that removing things like compassion doesn't necessarily remove things such as callousness.
How's that? You good now, champ?