What a wonderful thing you have done!!!
That poor kitty was being tormented.
It sounds like you are doing all the right things, especially letting him get comfortable in a smaller space first. Once he becomes more accustomed, he can expand his 'domain' in your home. Just do the best you can not to accidentally startle him, and visit with him in the bathroom often, so he does not feel that he is being punished by the lack of socialization. The fact that he let you brush him already is a great sign!
Good luck and kudos to you for providing two kitties with a loving, safe home.