Not silly questions at all! And also don’t worry too much, because all of this stuff is really guidelines, and it is very possible to bond bunnies in a range of circumstances. Some things just seem to make things go a bit easier.
You can start pre-bonding once he is healed from his surgery. Hormones in males will drop a long during the recovery time (about 2-3 weeks), and then continue to drop after that. You might see lots of pee and poop wars, but that should all get better over time. If he is still acting crazy hormonal 3 weeks after, you might decide to wait a little just to have less pee clean up to do, but it’s your call. And during bonding there can be lots of marking anyway, so no guarantee that waiting longer will be that much better.
They should def live side-by-side during pre-bonding if possible. So if I understand correctly, do all rooms in the house currently have a bunny in them?
If possible, once you start pre-bonding, I think it would be best to set up Tokki and Monkey in side-by-side pens in the bedroom that Monkey currently has all her “stuff” in. Then, every day or every other day, swap who is in what pen. In terms of exercise time, I have found it easiest to alternate who is free-roaming (so one bun gets all day, other bun gets all night), assuming they are both OK to be roaming unsupervised. Alternatively you can divide the space with fencing, but this can be annoying to deal with. You will want to make sure the pens are very secure, so they can’t jump in or out, and can’t nip each other through the fencing. I like using NIC cube grids for temporary bunny housing during bonding, and I found these “nose guards” that you can use to prevent nipping: https://binkybunny.com/forums/topic/nose-guards/
Now, Monkey will NOT be pleased about this, but part of the process is getting the original bun used to the idea that they are going to be sharing their territory. I think it will be easier down the line if you do the pre-bonding in the area that she views most strongly as her territory.
In terms of neutral space, I would choose an area that has had the least bunny activity and is farthest away from where you set up their pens. Bathrooms and kitchens can work well, because they are easier to clean and most buns don’t like spending too much time in them. Rabbits are very smell oriented, so the more unfamiliar you can make it smell, the better. I probably wouldn’t do anywhere the living room, even if you don’t allow her in, because it likely smells very familiar with the couch etc. But, I also wouldn’t feel bad about limiting Monkey’s space to just 1 room for a bit during bonding. The living room might be a good “semi-neutral” area, so it might be good to reserve it for that purpose. Remember it’s only temporary!
There may be some trial and error with the space. Worst case, start asking around for some friends that might let you do some sessions at their place. I used to live in a studio apartment, and I had a lot more success when I bonded away from home (vs. in my bathroom).
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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.