Jackson Galaxy refers to cats who love being up high as "tree dwellers". It makes them feel secure, especially in multi-cat households or those with other animals or small kids. Keep up the great work!
If he loves dry kibble then use that. Anything he loves and if he loves being pet also great. Anything to have him enjoy his time with her around either by scent or visually.
Anytime we can associate the other cat with something good is very helpful.
Same with the box. As long as he is not using it to hide but his playing with it is great. Anything to help his confidence.
Is it possible to have him occupied while he is in the other room? Playing or anything to get him distracted? To view the other room as a positive rather than a negative?
I agree with Tarasgirl, you are doing all the right things and love and patience are key. I would add be as calm and confident around them as possible as cats do take on our emotions. If we act like everything is fine then they tend to act a little calmer and more accepting.
But keep up the great work. And let us know things go and how we could possibly help.