Theory and Analysis:Eva-03's Soul

Although it is never directly stated whose soul resides in Eva-03, it is certainly Toji's mother's. The soul of Shinji Ikari's mother, Yui Ikari, resides in Evangelion Unit-01, and the soul of Asuka Langley Soryu's mother, Kyoko Zeppelin Soryu, resides in Eva-02. It is stated that Shinji's school class is actually a secret pool of potential Eva pilots, all grouped into one place. Also, it is gradually revealed or implied over the course of the series the mothers of all of Shinji's classmates are dead; (Kensuke Aida directly states this, and Hikari Horaki and Toji also heavily imply this). Thus it seems to be implied that there is some connection between all of the potential pilots having "dead" mothers.

Then, consider this, from the Classified Information:

A unit called a core is used to eliminate the discrepancies in Eva, a human being with the body of a god and a soul. The soul of the pilot's mother, which is placed within the core, acts as a medium and makes piloting possible.

Due to difficulties encountered in the development of Eva-00, the core's system is poorly constructed, and she falls behind in performance capacity as a result. Another reason for her inferiority is that Eva-00's pilot, Rei, does not have a mother."

This makes it plain that with the exception of Rei, the pilot's mother is always chosen as the Evangelion's soul.

Following this chain of evidence, the inescapable conclusion is that Evangelion Unit-03 contains the soul of Toji's mother.