And If That Don't Work?/WMG

The salvage operation didn't work.
It was a process geared specifically to be used for Rei (who has the soul of an Angel, not a human), and might not even work at all for anyone else. Misato and Shinji truly died in Chapter 1 and weren't able to be saved, and both have moved on. They're not coming back.

Misako and Shinju, meanwhile, have completely new and different souls. How Ritsuko even accomplished this is not clear, but in Misako's case she made a reasonable facsimile of Misato. Shinju, on the other hand, is so unlike Shinji that it is very obvious that something is not right.

Perhaps NERV was able to somehow capture Sachiel's (the third Angel's) soul, split it, and put both halves into two different bodies. They also uploaded Misato and Shinji's memories to them (they were able to save these before their deaths, but not their souls). Maybe it didn't even work correctly at first, resulting in dozens of failures, with the resulting botched Misako and Shinju having to be destroyed and all memories of these events wiped. Eventually, it succeeded.

They are completely different people, albeit in the bodies of Rei clones. Misato and Shinji are dead, and Misako and Shinju only think they used to be them. One or both will eventually see or remember something that they shouldn't have, and everything will unravel from that point on.

More characters from That Guy With The Glasses will show up.
The fic already has Insano. Why not have Nostalgia Critic and the others show up?

Lilith will be killed after awakening
We have angel-busting nukes, and nuclear powered machine guns that can kill angels. By the angels have resurrected their 'mother' humans will have enough firepower outside of NERV to blast her to pieces.