Well, I haven't watched the show through completely in several years, but still remember the gist of it due to years of writing and conversing in it's heydey. Honestly, it's just a pleasure to read from someone who has a basic understanding, as you do, and that's becoming all too rare. Your post was recent, and I was happy to contribute. I feel our theories sort of converge, but also may differ slightly. Hard to tell.
I think even Boone, Shannon, Nikki and Paolo had a flashback, and I naturally assume that whoever has a flashback or is featured prominently in several others' flashbacks, had been in contact, evaluated and eventually touched by Jacob as a candidate. I don't think everyone on the plane was destined to come to the island. Many were just unlucky and probably died on impact. Also, if you remember they found the pilot & co-pilot in the cockpit in the first episode, and they were mangled with only one being barely alive. The smoke monster (MIB) immediately kills the dude as a horrific show of power, and we know that's not possible with the candidates until they're eliminated from consideration of the caretaker position. So, obviously there were many who are essentially collateral damage. As Eloise Hawking would say, "death was their path."
Jacob and his brother, MIB, cannot harm each other, and the candidates are under Jacob's supernatural protection until they're not. These decisions appear to be communicated omnisciently. There is some kind of game or pact in place between Jacob and MIB, the former feels humans are essentially good and virtuous, while the latter is much more pessimistic and believes them to be inherently corruptable, evil and malignant. MIB, being a sleaze, tips the odds in his favor with this worldview by repeatedly interfering by inducing visions, terror and other forms of madness. Jacob is far more passive—like a deity that allows disasters and freewill, while still maintaining his righteousness.
Where we seem to differ may be with smaller points. Charlie joining Kate and Jack in the first trek of the pilot was essentially just him trying to find his stash of heroin dropped in the lavatory as I recall. I don't see this as anything meaningful in the story, regarding the relationships, if that's what you meant. Dominic Monaghan, though supporting, was one of the most well-known cast members at the time from his role in LOTR, so of course he had plenty of screentime early on.
I also don't feel the flash-sideways had anything to do with Jacob per se, but simply was generated by prolonged exposure to the Source of the island, electromagnetism, the stuff of life, etc. Whatever gave Jacob his godlike powers, also gave the survivors the ability to reconnect outside of time/space in a purgatory of death. Michael Dawson, father of Walt, didn't get to... but I don't believe it was necessarily because of his evil deeds or whatever... it was just that he left the island far earlier than most candidates and died in the perimeter on the mercenary ship outside of range of the Source. Mr. Eko was unrepentant directly to MIB's face. I believe he was deemed supremely corruptable, and eliminated from candidacy early. MIB tried to manipulate him some to perhaps endanger the others, but eventually just realized that it was fruitless and murdered him. This is sort of a sticky point of the series, since I believe Eko was supposed to be built as a *very* pivotal character, but some contractual agreement with the actor and showrunners fell through leaving some confusing loose ends. Eko never returned, not even for the flash-sideways.
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