Just curious: When you say "Greater Soul Gems", did you mean "Grand Soul Gems"? (That is how the Shade of the Revenant in Oblivion worked). Your explanation says you have too many grand soul gems and not enough grand souls -- a problem which has nothing to do with Greater Soul Gems, so I'm confused as to which one you actually mean.
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You mention the weapons with Soul Trap.
Bound Weapons have a vanilla perk under Conjuration that allows them to Soul Trap on hit. Are bound weapons supported?
Either way, thanks for sharing this.