Hello, my name isXXXXX and I have over 20 years of experience as a veterinarian.
You are very kind to take this fellow in, have him cared for medically and try to integrate him into your home.
His behavior is fairly typical for a cat that has been on his own and has had to fight to get food and stay alive. Cats don't live together normally in the wild. They have territories, although they are fluid, and will fight to preserve resources. Toms will tolerate females better then other males due to their drive to reproduce but once that is gone they may see other females as competitors too. Now that he is healthy and has more energy and has been invited into your home he may see that as his territory now and he may have decided to get rid of all competitors.
In many cases with unlimited resources in a home environment they learn to live together peacefully and some learn to enjoy each other's company. But some cats simply never learn to tolerate other cats in their environment. It is worth trying to get them to get along, but it may not work. Unfortunately because he's been on his own for a while and your females are quiet timid it may be more difficult.
Do they ever ignore one another and co-exist peacefully while in the same room or
does he react every time he sees them?
At this point I would never leave the three of them alone together when you aren't
around to mediate. And in fact you may want to start all over with introducing them again.
In aggression cases I recommend using a product called Feliway so I am glad to see that you are using that. It is a synthetic version of a feline calming pheromone and hopefully will help the girls be more confident and him a little more mellow.
There are also pheromone collars which may help calm them all. It's worth a try. See
this link: http://www.amazon.com/s/ref=nb_sb_ss_i_1_17?url=search-alias%3Daps&field-keywords=feline+pheromone+collar&sprefix=feline+pheromone+%2Caps%2C197&rh=i%3Aaps%2Ck%3Afeline+pheromone+collar&ajr=0
Keep them completely separated when they are indoors, behind closed doors for several weeks. That way they aren't constantly confronting one another but are able smell and hear one another and get used to having each other around in a non-threatening manner. Make sure to frequently switch bowls, beds, toys and use the same brush on all cats to get them smelling the same and familiar to each other. You can switch areas too so that none of the cats becomes too possessive of any one area.
Then try using a large baby gate between areas to keep them separated from each
other but able to see one another for a few weeks. If he is becoming aggressive
at that point and they are getting nervous again then you may want to try a
homeopathic calming oral medication called Bach's Rescue Remedy. See this link
for further information: http://www.bachflower.com/rescue-remedy-pet/
We want them calm enough to learn to at least co-exist.
If things are going well allow them in a room together, but only when you are present.
You should make sure that there are plenty of spots for her to get up and away from
him, such as cat trees or ledges that are carpeted and comfy to sleep on. Cats do tend to get along better when resources are unlimited. Make sure there are plenty of toys for everyone and don't let him harass them. If he isn't respecting them and does chase them or continually tries to approach them it's fine to use a can of coins to throw near him as he approaches or starts to chase for negative reinforcement. This must happen every time though for him to learn.
You may also want to feed them separately in different rooms so neither feels there
is any food competition.
If all else fails discuss anti-anxiety meds with your veterinarXXXXX XXXXXke Buspirone
or Amitriptyline for all of them as stress is certainly playing a part in this. If any one hates taking pills there are transdermal gel formulations of these medications available. These need not be forever, just long enough for everyone to learn to live peacefully, then gradually withdrawn.
Best of luck with your kitties, please let me know if you have any questions.