What you are experiencing is not uncommon. Yes, most times, two bengals can get along. And, why people think two bengals are better than one -- I don't know -- because this situation can happen and it tries your patience.
First of all, check out Jackson Galaxy's Spirit Essences and see if something will work in your situation.
http://www.spiritessences.com Second of all, you need to calm down and stay calm. The issue here is your dominant male. There is always an alpha cat in the household and he has made sure your little gal knows it. Thirdly, the bullying that is going on has caused your little lady to lose confidence. She is completely stressed out. That would make her spray or pee outside the litter box.
As for a solution -- you have a very large home. There should be enough space for both cats. Do they both have their own areas with cat trees? Do you engage both cats in play time at the same time? The key here is to slow down the aggression of your male and built up the confidence in your female. This means redirecting any aggression by your male by using toys. Jackson Galaxy has used this technique in his My Cat From Hell series. Know that YOU will have to do your part in helping these two. Re-homing is an easy word -- you have no idea how many thousands of bengals are currently looking for new homes due to behavioral issues with their owners. Giving up on a cat is never easy as you made the choice to take on another bengal. This is on you and not the kitties.
Your little lady needs reassurance that she is safe. Your big boy need to know that he cannot get away with hurting your little girl. Bengal cats can learn to play together, sleep together, groom each other. And a lot of it stems from how they were introduced early on. These two need to be separated when you are not home and you need to play with them and observe them together when you are home. Work with the two of them -- they can learn the word "NO" or "STOP." Asking them to work this out themselves is not going to work. You would not allow two toddlers to duke it out without interfering, would you? You literally have 2 TWO year old toddlers .... and if you are willing to put the time in now, it will pay off later, although this could take months.
The outdoor world is truly not where your little gal needs to be! She's already timid and a prime target for some predator. Also, in a three level home, you need a litter box on each level and at least one extra one on the level the cats use the most -- you say you have four, but .... since they are peeing everywhere, you can add more. One can never have too many litter boxes.
I hope you do not re-home either kitty. I see pathetic pleas from rescues trying to find homes for bengals. Many end up in shelters and are prime for euthanasia. And there is no guarantee that a new owner will be able to handle an alpha male either. Please, please, give these kitties a chance. I know you are at your wits end and you work full time, but please put in the time required.