Welcome to the forum and congratulations on your upcoming baby. I use Feliway and have for a couple of years. I don't know how well it works, to be truthful. My bengal still likes to spray every now and then in the house. But, I don't think it hurts to use it. They make a spray as well.
I can't find anything good online about getting a cat used to a litter box once it has been toilet trained. And a lot of professionals do not recommend toilet training. To me, it's just lazy people who do not want a litter box. It is not natural for a cat to use a human toilet -- just like it would not be natural for a human to use a litter box. You may want to try to get him used to a litter box once more if you aren't comfortable with her using your toilet. I always figured it would be fine as long as they could flush the toilet afterwards.
Since you have such a small home, I don't know that confining her to just a bathroom would be a great idea. A lot is going depend on how she is responding once you bring her home. Feed of off what she's telling you and act appropriately. It's wonderful of you to adopt her and give her a loving home without other cats. It will take some time for her to adjust, but I know you have the time and patience to see that she does.