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.
- Considering that Shinju seems to have memories from Rei 1 there is a bit of truth in this