Lets look at the values of the first hits in the T2 training hall-

Acheron-
Damage min: 107
Damage max: 160

Combuster-
Damage min: 94
Damage max: 141

Amputator/CIV-
Damage min: 82
Damage max: 116

However, you see none of those numbers The damage formula in question is as follows:

base damage * multiplier - defense = damage dealt

Or for combuster/acheron:

total base damage * multiplier - (normal defense + special defense) = damage dealt

So how do you use this to buff the weapons correctly?

Well, we know what damage max values we want for the weapons-

Levi damage max (new) = 160
CIV damage max (new) = 141

And we know that multiplier = 1.24ish, and we know that at this depth defense is 60ish

Base damage * 1.24 - 60 = 160 (or 141 for CIV/Amputator)

At this depth, base damage should be 178ish for leviathan blade, and 162 for CIV/Amputator. This gets us the following values:

Amputator/CIV damage min (new) = 102
Leviathan damage min (new) = 118

Yes, that's right. At zero damage, these normal swords would out-damage acheron/combuster. But that's at zero, and acheron/combuster are elemental/shadow, and have far greater ability, and will still be great, and given bigger buffs would overcome their normal counterparts in terms of neutral damage. The meeting point is just at damage max.

Obviously it's more complicated...

But what if the damage formula looks more like this...

(total base damage) * (multiplier) * (depth multiplier for weapons based on star level+heat etc.) - (enemy defense) * (depth multiplier for that etc.)

Well, we have the true damage values for the old and the new at these depths, and from them we should be able to get a nice ratio.

Current true damage in training hall depth (CIV): 142
Current true damage in training hall depth (Levi): 153

Leviathan damage increase percentage: 178/153 = 16%
Cold Iron Vanquisher increase percentage: 162/142 = 14% increase