Aggression and conflict problems like this are not rare, but can be tough to set straight. We do have some useful pharmaceutical tools to help out, though.
In addition to the usual measures (Feliway diffusers, multiple litter box and food/water stations to minimize unwanted contact) I have found use of paroxetine (Paxil) to be very helpful in intercat conflicts with aggression predominating and with secondary redirected aggression (where they go after any convenient humans).
My hospital mascot came to us as an apparent bottle baby, at the age of 6 months. We found out on day one that he HATED other cats. He also would violently attack nearby humans if he couldn't get to the other cat (a patient in a hospital cage). I originally put him on buspirone which is my go-to drug for inappropriate urination since it is a great anti-anxiety drug in cats. But he still had some increasing aggression issues so after several months of wishful thinking I took him off buspirone and started paroxetine.
He's like a new cat. He is basically "safe" now and very loving even if other cats are nearby. I don't think he'll ever be completely normal, but compared to how he was, this is orders of magnitude better.
So I am a big believer in paroxetine in cats with aggression issues. I have also started using it in select patients and they all do well with it and we do see improvements. It's not a cure, but it can get them through a rough period and back into their normal behavior pattern.