So right now if you craft a CIV you get 3 points of buff against undead, as a tradeoff for slightly lower base damage than the Levi. If you then go ahead and equip skolver+BTS, you get 6 points of buff against everything, including undead, meaning you do less damage to undead than you would if you'd just crafted a Levi in the first place.
My suggestion is thus: Make inherent weapon damage bonuses stack separately to gear-induced bonuses.
Example: CIV crafted with "Damage Vs Slime: Ultra" UV, and a player wearing other gear that provides, say, 4 points of damage buff (ie two elite slash modules, or full skolver), would result in 7 points against undead, 9 against slime, and 4 against everything else.
Example the second: CIV crafted with "Damage Vs Undead: Ultra" UV, player wearing gear that provides 10 points of damage buff (full skolver, bts, two elite slash), would result in 12 points of buff against undead, and 6 points of buff against everything else. That is to say, the weapon's inherent bonus caps at max (6 points), as does the bonus from the rest of the gear.
... i have no idea what you just said, but ima plus 1 this just cuz i wanna get a cold iron vanquisher ( i think thats what you mean by CIV ), and it sounds like you wanna make it better...