Ditto on the various disclaimers about referring to souls, spirits, essences, etc. in game terms only.
Another Disclaimer: Sorry it reads like a textbook, I tried to cram everything in there (lots of very interesting questions in this thread, I haven't had time to read the whole thing yet, but when I do I'll try to add anything I omitted that my little cosmology can explain).
The way I've run the correlation between mind, body, and soul has worked for me in the past without a hitch (quite a few questions, but all answered to the players' acceptance)
Body: A tool and a vessel, nothing more. The body serves to manipulate both matter and energy as the physical world (a world of physics, chemistry, and logic) understands it, and to act as a medium to which the mind and spirit may attatch themselves and interact with anything and everything (with a few exceptions like incorporeal beings).
Mind: A process of thoughts and stored memories. Without a mind, the soul cannot interact with the body, they simply don't speak the same language. The mind is unique in its ability to comprehend both the real and the impossible and communicate with both.
Soul: The supernatural portion of a living being. Magick is what the soul is made of. The soul, alone, is not magical the way my rules describe it, it is simply made of the same stuff, arranged in different ways (like a different atomic configuration or differing wavelengths of energy). Magick (as opposed to magic; a type of magick) is defined IMC as that which science cannot explain (thus magic, extra-planar existance, mystical forces, gods, etc. all fall into this category because some part of the thing is 'unreal'). Unreal and Magick are for the most part interchangeable, as are Real and 'that which science can explain' for the duration of the post.
The 3 parts together form a living being when the right energies and conditions are applied.
When other conditions are applied, the being can be separated, and parts can be altered, broken down, or destroyed entirely.
If the Body is killed, the Mind and Soul are severed and each go their separate ways.
The Mind remains where it died, near the body, in a dormant state, awaiting resurrection or the influx of sensation (with no body, the mind has no reason to work and shuts down until it does). Influx of sensation can include spells like speak with the dead, as the spell creates a link with magic to the Soul, requiring the Mind to translate the 'real' caster with the 'unreal' Soul.
The Soul begins gravitating toward another plane of existance. It's link to the 'real' world gone, it is drawn like a magnet back to the areas of high magick.
The Soul's gravitation is not perfect, similar to the streamers and trails of ionic plasma between a negatively charged cloud and the positively charged earth just before a lightning strike. In life, the soul had been sending streamers toward the planes, gravitating toward the mind/body/soul's alignment, and without the body acting as a shield of 'realness', the energy of the Soul zaps to another plane of existance when it's streamer hits that plane's streamer just right (the method isn't perfect, explaining mix-ups and other anomalies).
The Soul, after gravitating toward one area of the alignment wheel, departs to another plane and becomes a petitioner or extraplanar entity (and is given a new body, similar to an astral body, that is made of Magick-thus since both Soul and "Unreal" Body are made of the same stuff, they can bond perfectly without needing the Mind to translate for one another).
At this point, if the Soul or unreal Body of the petitioner is destroyed, both are destroyed, as evidenced by the fact that extraplanar beings cannot be resurrected.
Divine Bodies may be made of mostly magick and some real stuff, or mostly real and some unreal, or something else alltogether, causing a powerful connection to the energy of their Soul, since the Mind Body and Soul are able to form a more perfect union.
If the Mind is killed the Soul and Body remain together, since the bonding process was completed during the spark of life. However, without the Mind, they cannot communicate or exchange anything. The body dies or goes catatonic/comatose with no source of the mystical (i.e. unreal) energy that causes life to exist.
Charm spells work in a similar manner, supressing the ability of the mind to perform certain functions and forming an artificial, magic interface that the caster can manipulate.
Necromantic spells like animate dead take a dead body and either mutilate the Mind so that it can function with a dead body as a housing (intelligent undead), or replace it with a basic 'catch-all' mind (mindless undead). Undead cannot be resurrected while they are undead because the spell is preventing the mind from being able to work with a live body. Once the necromancy is removed, the healing process of resurrection can begin, rejoining Mind, Body and Soul.
If the Soul is destroyed, Mind and Body no longer have life, and both wither away and return to their base components.
If a Soul is removed but not destroyed, like when it is stolen or kept elsewhere, a magical bond is needed to continue feeding life from the soul to the Mind and Body (through wierd rituals, the enchantments of a phylactery, or a magic jar spell or whatnot). As long as this link is maintained, the mind and body can function normally for the most part.
Magic must be fueled by a Soul, but the Soul must use the Body as a conduit to the Material, which requires the Mind. When permanent magical effects are created, a piece of the soul (represented as experience loss in serious cases) is torn from the whole and used for the eternal fuel source. This spiritual cannibalization is the source of most magical experience loss (necromantic level drains use magic to mutilate a portion of the soul so it can't function with the rest)
Experience is a numerical value representing how well adapted your mind is to functioning with the Body and Soul in their current state. Most physical injuries don't alter the Body's current state as far as the Mind is concerned (nerve damage is the mian exception). Radical changes in the Soul's alignment charge change the energies it draws upon and sends to the Mind for it and the Body to use, thus forcing the mind to relearn how to function and resulting in lost class abilities, spell power, or experience. Destroying parts of the soul also causes experience loss.
As the Mind becomes more accustomed to translating for the Soul and Body in more situations, it is able to channel more energy between the Soul and Body, and able to do it faster and with more precision (which can explain save, attribute, skill, spell ability, class ability, and hp increases).
