Rabbits have incredible senses compared to us, so at this point it’s probably impossible to hide the rabbits’ presence from each other. Unfortunately, the behavior she is displaying will likely stay as long as that perception of him is here, so if you’re brainstorming actions to try and prevent it, it might be a futile effort. Something you can try is swapping clothes whenever you interact with him, so the scent isn’t on you as much, if she is biting you as a result.

What you can try in the meantime to maybe help them get acquainted with each other’s scents is swapping litter boxes and toys. It might help her get used to the other scent and maybe she’ll be less reactive towards it, but that’s not guaranteed.

Regarding whether to move him out of the house I think more so depends on what you think will be less stressful for both of them, and also you! A rabbit pooping around a lot doesn’t necessarily mean they’re stressed. To an extent, there might be chronic, low stress, but if it’s tolerable until bonding can start, that is something to accept. Prebonding by swapping stuff now might help, as mentioned. It’s good to hear the pooping is decreasing.

I think the set-up sounds fine, and with more time she will probably settle down a bit. The pooping might not get better until they are bonded though.

I think it can also be helpful to think about “good stress” vs. “bad stress”. Another rabbit in your territory might be slightly stressful, but in my mind it constitutes a form of ‘good stress’ which can be somewhat enriching. Bad stress would be something like a dog or predator harassing a rabbit, or super loud construction noise, something that makes it fear for its life. If she was upset to the point of not eating or being very aggressive, I would think about modifying things, but it sounds like normal female bunny behavior when a new rabbit shows up.

Hopefully pre-bonding will go smoothly once he’s neutered!

You should start to think about what you will use as neutral territory for bonding. For set-up during bonding, you might find it helps to set up side by side pens where the rabbits live, and swap sides every day. This will help Monkey start to lose track of her territory and even the playing field a bit.

It can be really hard restricting a free-roam bun’s space, but they will adjust, and it’s only temporary!

My go-to arrangement is usually to build temporary NIC cube condos, and then I found these “nose guards” recently that are really helpful for making nip-proof barriers. https://binkybunny.com/forums/topic/nose-guards/

It can also be really helpful to block visual access between buns that are being aggressive towards each other, so that they get used to their scent first. Then you can slowly remove the barrier and it usually goes more smoothly. Once Toki is a couple weeks past neutered you could start litter box swaps and see how that goes. You might even try to use a surrogate stuffy with Toki’s scent on it. You can give Monkey the stuffy and let her attack/sniff/mount it, or whatever she wants to do. Some members have had a lot of success with that, as it lets the more aggressive bun get their frustrations out safely!

I think unless behavior gets worse you’re probably ok to leave them how they are. I have 3 rabbits and 1 of them has to be  separated and they were all really aggressive at first but it got much better with time. It will be worse for both rabbits until he’s neutered but it isn’t necessarily the end of the world! If Monkey starts chilling out some you can start with various prebonding activities, and if she stays a little on edge for now that’s ok too since he’ll be neutered soon, as long as neither one seems to be on the high stress setting all the time.