You could've just replaced her pistols with the E-11 from Ewok Hunt and assign completely custom damage values that wouldn't affect any other AI character.
For the E-11D the only options you have is the Death Trooper's E-11D or the Assault's E-11D. For most unlockable weapons there are add-ons that affect the damage of the weapon and therefore have a completely different file but the E-11D has no such in-game add-on, so you're limited to just those.
You have to go to U_ISBAgent_DualRK3 and replace the W_ISBAgent_DualRK3 with W_(whichever weapon you wanna replace it with). Idk how you were able to replace her pistols with an E-11 with that technique but weapons are for the most part replaced in the U_(..) files.
Oh yeah, that was the first thing I tried. But i think since the ISB's dual wield RK-3 works differently, it just changes her two weapons into one E-11, while still holding it akimbo/dual-wield style. This was the case even after I modified her KIT. So I just ended up giving her the Rocket Trooper's E-11 ability in GP to replace her RK-3 ability, which kinda works.
That is indeed odd. I never changed the ISB weapons specifically but I've changed several other weapons and it pretty much always applied the correct animations except for the sentry gun and melee weapons. Even when I switched out the main weapon with a grenade the animation still looked correct.
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Edit: nevermind, works fine