[@Savo]: Okay, have to get into some stuff that was too involved to include in the OP now. ^^;

Souls in my setting are technically referring to the "life" of something. The soul exists long before any sort of consciousness does, the moment something qualifies as alive. What people would consider the soul is more a combination of the consciousness and the soul. The consciousness is formed by a person, well, actually being a person, it's their personality, thoughts, and memories.

This means, for example, that a true ghost is actually the consciousness combined with some portion of the soul. This also means that a soul taken to create a homunuculus("recently dead" is all that's required and can be gained from going to a morgue or, well, killing somebody) is just life energy, just what caused life to come to that person. Which is also why you need it to make a homunculus since they need something to make them alive.

Now, this doesn't totally shoot down your character. Severely botching the transferal of the soul might accidentally nab the consciousness.