This hasn't achieved consensus, so you can do whatever you want, really. The only comments I have are from non-final sources: theres only one kind of souls, trapping a soul is temporary, when you use an enchanted object, the soul slowly slips out, and human souls are different from animal souls in some way. As for the soul gem issue, I'd say that there are probably multiple kinds - to explain the differrent models, and to avoid any conflicts with future lore.
Sounds like a great mod!
I think that the only real difference between the souls of the playable races and that of others like Falmer, Goblins, Giants (Who are all sentient in one form or another) is the protection of Arkay.
In Oblivion the reason for black soul gems was the Shade of the Revenant, when Mannimarco eclipses Arkay and that allows the ritual to take place.
Interestingly, the
ghosts of playable races in Morrowind can be soul trapped.
I think a soul gem might be like a cage of Faraday in reverse, keeping things in not out.
The soul itself does not seem to be used up, destroyed, when used for enchanting, more like a 'motive force'.
When you use a battery powered torch, you have not harmed the electricity when the battery has run out either.
There is no hard evidence for that, but there certainly is no evidence that souls are harmed or destroyed in any way. Youd think that would have been mentioned by now if it was.