You do indeed have a few things wrong. But first of all, the primary question about Largo's imprisonment. Largo wasn't in prison for that long a time. He was only in prison for maybe a few days, if even that. While the movie does hop between present and various flashbacks at times, it does so in closed self-contained packages. But the scenes in wherever Largo is at the beginning are heavily intercut with the scenes in Hong Kong shortly after Nerio's death, neither do they bear the "X years ago" tag that all the other flashbacks have. So this prison time certainly wasn't a flashback but happening concurrently. Besides that, we actually see Largo at the coffin of his father, so he got out of prison as soon as Nerio died.
He also never mentions "3 years" when he talks to Léa in the massage scene, only that he was sent to prison. What he does say, though, is something like:
After she got me arrested, this girl told a friend where to find me. [which refers to Freddy]
It is true that he hasn't seen Nerio and everyone else for the last 3 years, but that's not because he was in prison, but because he distanced himself from Nerio after he couldn't find his adoption files and thought Nerio kept them from him.
It also wouldn't make sense for Nerio's death to happen so long before the movie's primary storyline, since a major aspect of the story (and Ferguson's plan) was that it was quite urgent to secure the company's future and the trust of the shareholders shortly after Nerio's death, especially since there were acquisition plans from Korsky. The company was in a state that it couldn't have been in for years, if even weeks. It would also not make sense to inform Largo that long after his father's death, since Freddy always seemed to have a way for finding Largo and they would have searched him as soon as Nerio died.
Goran didn't get involved with Ferguson as soon as he found his files in the orphanage (which was 3 years before the main events). We don't exactly know what he did, but nothing much of relevance, other than maybe being angry at his parents and everyone else. It also wasn't Goran who had this whole idea, but Ferguson. But she only made her plans once she learned about Goran and Largo and Nerio's illness. Then she planned everything, she played Korsky into threatening the company with an overtaking, got in contact with Goran, killed Nerio, and made Largo go to prison.
Which also brings us to another part of your question. Largo was sent to prison because Ferguson didn't want him to lead the company, which Nerio always planned for him. So she got him out of the way (or at least discredited if he would ever get out) and organized herself a better heir who would be more in her interest, since she knew what kind of "free spirit" Largo was and that Goran was much more willing to "behave".
Freddy: Was killing Nerio in the group's interests?
Ferguson: He was sick and dying. You know that...I had to keep control of timing. I'd never leave the group in the hands of some wild adventurer like Largo...The only person who can take over from Nerio Winch is me.
Goran: He told Ferguson everything. Ferguson found me and she offered me much, much more money than he did. On one condition. That I head the group and be content with the dividends.