Depending on your space and budget, cats feel safer if then can get up above the floor. There are shelves made for cats that you can mount on the wall, or make walkways up near the ceiling that go around a room, etc. You can look up that type of thing on the net. I'm thinking the stray cat had safe places to go when she was outside and now she doesn't. It's safe to you but not in her mind.
Cats are very territorial, so having two that did not come into your home at the same time can be difficult. We have two cats, one is the son of the female, and he dominates the living room and she gets the kitchen when they are downstairs. Upstairs they each have their favorite bedroom. They have worked that out fortunately, but when the female wants to get to the kitchen she has to pass through the living room. They don't battle, she just gets chased, but she also instigates alot of it herself.
Look up Jackson Galaxy on the net. He is a cat behaviorist and has a show on Animal Planet. He goes into people's homes that have cats that seem totally impossible and helps them to make their home a place where the cat feels secure, and then the behavior changes.
Really cats may be domestic, but they are little wild animals that live with us and let us stay because we feed them.