Yui's soul is deffinately inside unit zero one. In the Manga series of EVA,
there's an image of Unit Zero One with most of it's face armor not
installed. The image was used to describe what happened during the
experiment.

As for Unit Zero Zero, There are two things that we have to keep in mind,
it's original and it's soul. Zero Zero's body is made directly from Adam
(thus the name of the Evangelions, called EVAs, and EVA is Eve in german),
thus it might be a type of internal hatred against humanity which is inside
of it. As of the soul, i think it would be Ritsuko's mother. Contrary to
some posts on various forums, her soul does not make up the base of the MAGI
system, infact the Magi's are programmed to have artificial intelligences
that reflect the personality of it's creator. Unit Zero Zero openly attacks
Rei and Gendo. Ritsuko's mother felt that she was only an instrument in
Gendo's hands, that he betrayed her. Rei was only the example of Gendo using
her in his plans. That should be the reason why Zero Zero goes beserk for a
few times in the series (when shinji is in it, i believe that she not only
wanted to get revenge on Gendo, but also show Shinji some of the truth
behind Gendo's doings.

One interesting thought is, Why did Yui do the test on Zero One, and not
Zero Zero? The prototype was created mainly to test the feasability of
cloning and the developement of neural interconnect systems to be employed
on future EVAs. As for the Test Type, it's goal would be to create the
benchmarks that would be used to help in the selection of the future pilots.

"AEC" <hollowine@grandecom.net> wrote in message
news:hollowine-BA959E.22530930052003@corp.supernews.com...
> If the soul of Shinji's mother is in Unit 01, and if Asuka's mother is
> in Unit-02, then whose soul is in Unit-00? And why did it keep going
> crazy when it was initially activated?