I m sorry to hear about your large, male, young cat bullying your small, timid female.
Are there other cats in the home that he gets along with and plays with?
Is either cat allowed outside?
Is he a fellow with lots of energy?
Although his behavior may seem sexual, it may or may not be. Dominance behavior in cats often appears sexual as the dominant cat may jump on their poor housemates back, grab their neck and make lots of noise. The lower on the chain kitty may scream and holler in protest and fear, and as a way to try to get the attacker off. Either way this is no way for your little female to live.
Cats don't live together normally in the wild. They have territories, although they are fluid, and will fight to preserve resources. 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, and some large, very active kitties may get bored and bully their housemates.
It is worth trying to get them to get along, but it may not work. Unfortunately because it's been going on for an extended length of time it will also be more difficult to fix.
Do they ever ignore one another and co-exist peacefully while in the same room or does he react every time he sees her?
At this point I would never leave the two 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. It is a synthetic version of a feline calming pheromone.
There are also pheromone collars which may help calm them both. 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, 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 both cats to get them smelling the same and familiar to each other.
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 she is 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. They should be small enough that only she can fit, so he doesn't have room to maneuver and attack her. He can have lower areas to comfortably hang out on, but she should always have the option/ability to get away.
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 her. If he isn't respecting her and does chase her or continually tries to approach her it's fine to use a can of coins to throw near him as he approaches her for negative reinforcement.
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 veterinar***** *****ke Buspirone or Amitriptyline for both of them as stress is certainly playing a part in this. If either one hates taking pills there are transdermal gel formulations of these medications available.
Finally he may do better when allowed to go out so you may wish to construct an outdoor cat pen so he can safely spend time outside. Here are some examples:
If he seems bored perhaps introducing another male his size for him to wrestle and play with may take the burden off her. Make sure the new kitty comes on a trial basis though just in case that turns into another bullying situation, or they both gang up on her.
Best of luck with this situation, and let me know if you have any further questions.