Actually, hold on. Let me try and make sense of this "continuity" of mine. At least since the original run of stories ended, with Shinji in Kaworu's clutches forever as Mari walks away from them.
This "second run" of stories seems to have the following setup:
Spins off of Episode 24, "The Last Cometh," and Kaworu's appearance and subsequent connection with Shinji. This is where the canon of the weight gain stories diverges. In THIS version of things, Kaworu successfully seduces Shinji to run away with him. This also involves Kaworu himself running away from what SEELE expected him to do, which was to touch Lilith and start Third Impact.
In the aftermath of this, I assume Unit-01 shuts down completely, Yui having realized that, at least for now, there'll be no going forward with the Scenario. This scuttles the plans of both NERV and SEELE, and there's probably some big political calamity with the entire Global World Government run by the UN. There's some kind of chaos, what I haven't decided, and NERV collapses, taking Tokyo-3 with it.
In the ensuing chaos, Rei comes across Asuka in the bathtub before Section-2 does, and decides to run away with her.
Misato somehow comes into a lot of money (probably steals it as NERV collapses) and decides to abscond into "retirement," taking Maya, Makoto, and Aoba with her.
Ritsuko also escapes.
Understandably, Gendo and Fuyutski's whereabouts are unknown, and that's probably just how they like it, at least for the time being.
So, everyone who escapes the ruins of NERV makes it to various parts of the United States, perhaps all in California since it's on the West Coast. I've always figured Shinji, Kaworu, and Ritsuko are in Northern California in their stories, with Asuka and Rei in some other part of the state, and Misato maybe further down in Southern California, closer to Los Angeles.
And after the passage of a few years, Shinji, Asuka, and Misato have all gotten really, really fat, under the grooming guidance of their various caretakers.
Under this scenario there's no need to account for Kaji because he'd already be dead.