Being able to add a level above Grand would be the ideal, however, if that is not possible..... you present some interesting ideas on how to get around it. Don't know much about XML yet though, so, trying to figger out how to convince the enchanting menu to allow more than one soul gem might be interesting... (I see a steep learning curve in my future.....) As for equipping them from inventory, intercepting the 'recharge' menu, and giving a choice of recharging, or ADDING to max charge shouldn't be out of the question. Might have to look at that as an alternative.
Looking in the CS, I don't see anything that specifically notes an item as a soul gem..... but, maybe copying an existing one, and changing paths for the model, icon, and such might have it categorized as such?
I suspect that the Soul Gem for Arch Mage Traven's soul was purposely done as a misc item, so that you COULDN'T use it for enchanting something.