Welcome to BB! It’s really great you are planning ahead!
I have a couple suggestions. 🙂 First, I would not use your room for bonding sessions. No matter how much you clean it, it won’t be neutral enough as a starting point, especially since Kyoshi has had free roam of the room. Is there anyway you can set up temporary pens in your room? What some people do is build a pen for the new bun in the same room, and use nose-guards (https://binkybunny.com/forums/topic/nose-guards/) or a 2 fence buffer to prevent nose nipping, so original bun starts out still free-roaming and new bun is in the pen. Or the original bun can also be in a side by side pen. After new bun has had some time to settle in (a week or two with no side swaps), you can start swapping sides every day or two. Kyoshi will very likely be mad, but that is honestly kind of a part of the process. You want Kyoshi to sort of lose track of his territory, but also realize that the new bun is not hurting him and he’s still getting food, etc. Often after even a week of this you will see big changes in behavior and they will both become much more relaxed towards each other. It’s also OK if their pen size is a little smaller than you’d normally like during this time, it’s temporary!
What I did when I lived in a studio apartment was I had both buns in temporary NIC cube condos, and then I would alternate who got free-roam time (so one bun got exercise in the morning, the other in the evening, for example).
Then I think you should do your bonding sessions in the basement, since it’s completely neutral. You can set up a pen down there and put some protective flooring down, and it will work great.
I think this will also be good because it will let you bond with the new bunny more easily, and Kyoshi won’t be lonely in the basement.
Once they are doing well in bonding sessions in the basement (as in they are seeming pretty much bonded), then you can clean and rearrange the room again to be their final home together.
I’m also not sure what you meant with this sentence, “At night they would be enclosed in the same pen but only have access to about 4 ft by 6ft.” I think I must be misunderstanding, but just want to clarify that they should never be together unsupervised until they are 100% bonded.
Be prepared for Kyoshi to be pretty grumpy at first, and likely during the bonding process. But don’t worry, he will forgive you!
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.