Nice, thanks for posting it!
Ah, I with there was more Rei in it though. Or, ideally, the whole story focusing on her in the first place... oh well.
Anyway, one thought occurred to me while reading: when Asuka wakes up and wonders where is Shinji, wouldn't it be nice if it wasn't Misato who decided he gets butchered too, but Shinji himself? Like after having sex with Asuka he sympathizes with her and thinks it would be a nice thing to do to get butchered too because it will make Asuka feel better. And because it's just bothering him to get special treatment, like he kinda feels guilty about it. And speaking of Shinji, you say they chopped his dick off and discarded the body, but wouldn't he still be alive? Maybe bleeding out slowly. So if they don't need the rest of his body, maybe he's just sitting there watching the girls get butchered while he bleeds out. That would be a nice detail.