Probably the only aspect of the next section, Gendo, Rei, and Ritusko in Dogma with Lillith, I need to comment on is the alteration I made to the actual events. In the original, as you may well know, Ritsuko just stood up, she never approached Gendo. I couldn't have her get shot (read I didn't want her to be), so I simply gave her a little attitude (just a little) more than she had in the actual scene in End of Evangelion. Also important, at this point I don't try to 'develope' any of the cast members outside their series molds, so Fuyutsuki is still very much 'on Gendo's side', if that phrase can been seen as accurate. From the anime, I sensed Fuyutsuki was simply facing what he percieved as inevitable. It is that very inevitability that this fan-fiction starts to change, and so I hope the plot's effects on Fuyutsuki in the future are believable to even a die-hard fan who hates the idea of messing with the original creation.
The first time we see SEELE in Kenosis is a good taste of how they'll be for the rest of it. Watch the anime enough times, and you'll be able to spew SEELE-dialogue out without even thinking. Simply never say anything specific, refer indirectly to everything, and have some arrogant debate. The only facts I had to keep in mind were the differences between Gendo's plan and their own, and the attack on NERV. From here out, my own plot gives me the fodder for their dialogue. Similarly, Gendo and Fuyutsuki's interactions are easily archetyped in the 'vague, know everything' chats. Half the reason Evangelion was so hard to understand was because of 1) misdirection through narration, and 2) no one ever clearly states anything until the end of the series. I take the same rules, especially 'misdirection', and continue to use them, only now the roles are reversed. SEELE and Gendo have no idea what to expect, and I, the author, do. Using the character's ignorance makes my story look much more mysterious than it really is.
Shinji and Asuka's interaction is obviously just keeping them in the picture and explaining why they pop up later as a good little author should. It's also a character-interaction excuse, and characters are the core of my writing enjoyment.
It might surprise the reader to know that I never even hesitated, paused, or had to think about how I'd bring Kaji back into the story. Him waking Misato up (his death and her gun-shot wound both modified before my story started) flowed as fast as the battle that started Kenosis off. I figured he'd be watching the final battle, however it went, so having him close enough to recuse Misato felt natural. The reader may find it too convenient after already screwing with the original plot. And of course, more character interaction is always fun. It's what makes the story enjoyable rather than an outlined plot.
Naturally, I finish the introduction with foreshadowing. The best kind of foreshadowing is ominous foreshadowing, even if the intended result will actually be a good thing. As for the person implied by 'we already have one of those', I can't dicisively say who it is aside from whoever shut down Tokyo-3's power in the series. Kaji is one possiblity, it could also just be some random person we never see, simply a faceless extension of SEELE's authority. Both are possible, and equally likely. However, I personally doubt it was Kaji.