First of all, you need to make sure there is nothing medically wrong with your male. Check out some of Jackson Galaxy's Spirit Essences.
http://www.spiritessences.com. There are many products that may be able to help you and there are people who swear by these. It takes a lot of patience to modify a cat's behavior. The fact that your male has become so aggressive toward your female happens sometimes. Your girl loses confidence and becomes a different cat. What caused your male to start peeing and marking inside the house? Well, sounds like there is something going on outside your house, which is why he wants to go outside. Are other cats coming around (stray, unneutered)? You may not ever see them, but your male can sense they are there, thus he wants to get outside.
I always thought a screen porch was a great option, but I've had cats who clawed holes in them. Once a cat has tasted the outdoors, it's next to impossible to keep them from wanting to get back out there. If you have a yard or a deck, check out cat enclosures. Just googling will provide you with hundreds of images of different types of enclosures. We built a 12'x12'x8' high enclosure on our deck for Raiden. It is escape proof and he enjoys being out there. You can always try to get your male to walk on a harness and leash. The only problem with that is the cat wants to walk all the time. Now that I'm retired, Raiden goes out twice a day -- early morning and late afternoon. He still would rather roam free and does escape through the front and back doors at times.
A lot of people recommend trying to re-introduce the cats, but I'm not really sure that will work because the environment that is affecting your male has not changed. You may simply have to keep them separated for a while. I do recall an episode of My Cat From Hell where there were multiple cats and a few did not get along. They had to catify their house so they had places for all the cats to be. This may mean multiple cat trees, shelves on the wall, stacked crates -- where your cats can each have their own space. The cat super highway cannot have any dead ends. Your female will always need an escape route. And you need to be playing with each of the kitties. Bengals are high energy, and males are highly territorial (especially if they see other cats around the outside of your house).
If you can finally satisfy your male's need for outdoor access, you should find the marking, peeing will stop. Our cat enclosure has a cat door that allows Raiden to go out there 24/7. He will mark out there, but he does not mark in the house. We did have a neighbor's cat who would come around to terrorize Raiden when he was in the enclosure, but they moved away and now things are back to normal again. So make sure there are no other cats coming around the outside of your house.
I wish you a lot of luck here. Your little gal is depending on you to keep her safe.