Ms. BonJovi, I'm not a Matrix/Linda expert, but certainly the "merging" created a new lifeform with Supergirl's powers and Linda's (albeit tainted) soul. Was this merging "scientific" or "spiritual"? Hard to say, considering that Matrix probably had no conscious intention of combining her artificial lifeform into Linda's dying body -- she just wanted to save Linda in any way possible. Such a selfless sacrifice alone could produce an Earth Angel, but since this act of salvation occurred in the midst of a satanic ceremony one wonders if this interplay of Good and Evil forces helped produce this "miracle".
As Matrix/Linda questioning her identity/identities, on one level this is understandable -- who's REALLY in the driver's seat? It certainly appears that Matrix is predominant in the beginning, but along the way as more of Linda's memories resurface the distinction blurs. Is Matrix simply assuming the identity of a dead girl? This is certainly a distressing thought, since Matrix had promised the Danvers that she would rescue Linda, not impersonate her. Or as Matrix comes to understand Linda more, does she allow Linda to assume control so she will have the opportunity ("free will") to atone for her past sins and "redeem" her lost soul?
Matrix had earlier questioned whether an artificial non-human lifeform could possess a soul. After the merging, Matrix provides the "body" for Linda's "soul", but still there seems to be two conscious beings in play. After the separation in Issue #50, Linda feels an emptyness that's not entirely due to her severely reduced powers. But at this point Linda is her own person. When did she "recover" her own soul? Was it in Issue #50 or later when Linda sacrificed herself and was restored to life? I suspect the latter, but admittedly my direct knowledge of this series is incomplete at best.
I somewhat hesitate to suggest this, but you might find better Matrix/Linda experts on the DC Message Boards, particularly the Supergirl board at
http://dcboards.warnerbros.com/web/forum.jspa?forumID=29209082. Be warned that compared to the welcome civility in the Superman Through the Ages! Forum, the DC Message Boards can be a "rough neighborhood". There are some particularly boorish posters in the Supergirl boards who I will not identify. However, there are also some Linda fans who are well-spoken and very knowledgeable. You might want to post your question there, and hope the thread doesn't get hijacked in one of the ongoing flame wars.
Again, good luck with your project.