OK, I've finally got around to reading through it in more detail. The general concept is fine, and it's definitely getting interesting, now that Caster's plans have gone completely up the swanny. I'm also interested to see how Sakura ended up as Caster....
I do have a few comments, though, mostly typos or things I didn't understand.
Firstly, III A mentions a psychopathic comment to Lancer, but I can't work out what comment you mean.
Secondly, Caster's reasoning for continuing to attack Shirou even after he's down seems really quite odd. She really has no reason to kill him at that point (even not knowing he is Shirou), since the Geas is done and he's no danger to her. It just seems like it's a bit contrived.
Thirdly, you talk about "explosively-unlocked gates"? Do you mean Caster's shot blew them open? If so, then how did it not kill Shirou if he was heading for the door?
Fourth, where you say "She couldn’t faults his choice", it should be "couldn't fault his choice".
Fifthly, what does "opalescent" mean?
Similarly, "newborn darkness" doesn't make sense, really.
Also, where you say "she wasn’t surprised that he had just survived two miniature, arrow-mounted claymores at point blank. ", it should be point blank range.
Also, I think there's something slightly wrong with (normal) Sakura's characterisation. In her flashback, you make it out as if she thought if she hung around Shirou long enough, he would fall in love with her. In reality, that's not true. Sakura never expected Shirou to fall for her, she has too low self-esteem for that. Further, she didn't even want him to, at least on a rational level, because she knew that it would put him in serious danger due to Zouken. Ultimately, she was just happy to be with him at all. Even if emotionally she would have liked to be something more, she never expected it and she believed it wouldn't be good for him if it happened. She certainly didn't "wish" for it, at least not in the sense of actively desiring it to happen.
Finally, another typo. Where you say "with only a crater in the floor being proof that Emiya Shirou had ever existed", it should be "as proof".