Does anyone know how to edit the effect of weapon mods? I know you can change their value with the GECK, but how can I change their effects? For example I'd like to add a bonus to the scope mod giving it increased accuracy in VATS. I might also try to fix the bugged laser rifle splitter. Is editing these done with a script? Is it even possible?

No.

NVSE adds a GetWeaponItemMod control. I'm hoping this can be used to script a mod kit function. Add a mod kit with None for the effect, then use the NVSE command to detect the kit and apply a scripted effect.

Haven't tried it you, so may not work.