So Ive been playing the Zombie apocalypse mod and its great but just isn't what I want it to be. What I want to do is take a vanilla NPC, Moira of Craterside Supply for example, and apply a texture overlay much like the blood splatters then change her animations & behavior based on a script for this zombification effect.

Is it possible to take a regular NPC then modify the skin/texture on this NPC (say a pale overlay texture to give the look of death but retain the other physical looks of the npc, including what was equiped, hair, etc) then give it custom animations? The ideal would be to do this on the fly to allow a 'cure' or some such reversal of the effect via script. Im just wondering if this sort of thing is possible and if anyone knows of some article or something that could help me do this.

Can't change animations on the fly. You can cripple both their legs to force them to stagger and equip a weapon with the zombie animations copy-pasted to be it's attack animations, though.
You could use ChangeRace to alter them to a Zombie version of the existing race then changerace them back when cured, but you'd need to check a flag in the GECK to make that possible.

cool, i think i can do that. How about graphics? is it possible to add a layer or something like that on the fly?

I think Toaster was talking about that with the changerace bit. An alternative would be to use an effect shader.

Playing a shader that affects skin only doesn't really work, it only affects the head. The easiest way to change skin colour is to change race.

After looking through the GECK FAQ I just can't figure out how to cripple an actor. I have my test ghoul in the game but is this something done via script?

Changing race would make the NPC lose the look and gear wouldn't it? One of the main reasons to do this is to keep the effect of the NPC now a zombie. Such as if Moira, being happy and such, gets infected then turns into a mindless zombie.. still looking like Moira and all, hence the shader idea. I think just applying a custom shader much like blood would work for the effect.. I just don't know where to start with this.

To make an actor cripled, damage their limbs like this:

actor.damageAV LeftMobilityCondition

See http://geck.gamesas.com/index.php/Stats_List for other "limbs"

thanks, that works perfectly. How do I go about swapping animations? I can't find anything except how to make them.

Just find the ghoul animations you want to copy, and find the human animations folder. Copy the ghoul animations and rename them to fit missing slots in the animation set. For example the 1 hand melee sets are 1hmAttack3, 1hmAttack4, 1hmAttackLeft and the like, so find an animation that one weapon type has but unarmed doesn't and rename the animations to fit it. Then open them in NifSkope and change their controller name to match (so if you copied a ghoul's attackLeft_slash.kf to unarmedAttack5_slash.kf, you'd need to open it in NifSkope and change the bit saying "AttackLeft" to "Attack5").
Just a note, if you have an attack5_chop, attack5_slash, attack5_anything then when a weapon uses the Atack5 animation it'll pick one of them at random.

Awesome, I will try this when I can. Im sure this will take quite a while but I think it will be worth it. Someone mentioned shaders? I searched but did not fight much more then texture sets, is this the same?

No, an effect shader is something different than a texture set. An effect shader applies an effect over the top of the model and its original texture(s), while a texture set is used to change the texture that a model uses.