I had to respond to this one, since I have been around a few cats in my time. You've already had a lot of good comments, but I have a couple more very specific suggestions. The first has to do with making friends with your cat. If it was ferral or raised by a ferral mom, it probably was making do by hunting. I had a cat that we got from the shelter when she was a wild "teenager" cat. We kept her in an enclosed room (the laundry room) for a while until she knew she belonged to us. Then she was allowed further into the house. She really was quite frightened of both of us. My hubby used to say she wouldn't warm up to him. The thing she missed the most was "catching her food" I figured this out when she adopted a length of binding tape (about 24") from my sewing room and every night she play with it and drag it down to the kitchen beside her food dish. The next morning, I'd put it away (on the floor of my sewing room) and then she'd repeat the gig the next night. Then, I started playing with her with the binding tape, and she had a great time. So when hubby said she wasn't warming up to him, it was because he never played with her. When he started relating to her on her terms, they became fast friends. Only later was she able to accept petting and other affection, as she gained a trust in us.
The second issue is the one about the litter boxes. In my younger years, I thought that the important thing to clean from the litter boxes was the poop, but I read in a book, and it made sense to me that the urine is also so important to keep out of the box. Animals do use it to mark their territory, and if another's urine scent is there, the area should be avoided by another cat. The author suggested that the urine forms a little mountain shape in the box, with the top of the mountain at the point of entry, and the base at the bottom of the box. She suggested keeping the litter box somewhere you pass often, and just check it and clean urine up as soon as possible. I found that clumping litter really makes this process very much more easy. And when we had two cats, it was helpful. I also did find that they did better with each their own box - still cleaning about as often as we flush. A small price to pay in labor for the great companions they have become for us. Good luck!