First, the good news is that 3 weeks isn’t that long, so the neuter still has time to knock some of those hormones out. I would say you need at least 4 weeks, but 8 weeks is probably a closer guess.
Second, has he been thoroughly checked out by a vet to see if he is in pain? Particularly his teeth and ears? What breed is he? I wouldn’t normally ask that, but it sounds like he went through a lot to get to you so maybe he came from a special breeder. Is it possible he comes from a line of severely inbred rabbits? Was he transported in the cargo hold or cabin of the plain? If it was the cargo hold, his ears might have been affected.
Third, when you first brought him home did you automatically give him free run? If so, that might be part of your problem with litterbox training. One of the best ways to encourage good litterbox habits is to section off an area of the room with an expen. Make it pretty small for the first day or so, and then slowly make it bigger as his litterbox habits improve.
Fourth, are you going to him, or do you allow him to come to you? What if you just sit on the floor with a treat for him? Does he only attack your hands, or does he attack any part of you? Have you tried squirting him with a squirt bottle when he charges you (assuming he isn’t cornered)? Have you tried stomping your feet loudly and turning away from him?

My girl used to charge me when I walked around my room. Stomping my feet seems to work the best in order to get her to stop. Otherwise, I pretty much ignore her. I give her a treat after she lets me pet her nose, or if I do have to catch her to groom her. I also throw a treat in her cage when I want to lock her up. I try to do very little handling with her as it makes her less trustworthy of me. I never pick her up to cuddle, or just because, I only hold her because I have to do so.

Please remember that rabbits don’t respond to dominance or discipline like dogs. A rabbit would never pin another rabbit to show dominance, or for that matter, pick another one up. I am sure other members will come along to offer more/better suggestions and better rabbit language advice.

I’m sorry to hear you are having this problem with your bunny.

I agree with Kytkattin: Try making his area smaller. This will probably help with the litter training and may make him feel more safe and secure to have his own little area. Rabbits that attack are either defending their territory or are scared. What about making him his own little condo?

We have read that sometimes animals can just have a bad personality and it just doesn’t work out.

I’ve never met a rabbit that is just truly mean at heart. There must be a reason for the aggression.

Nose tapping or any physical interaction as punishment is probably making him more afraid (even though I know you are not hurting him). When my bunnies do something bad, I find the best method is a loud hand clap and a verbal “No”.

Don’t give up on him. I very much doubt he’s a mean bunny. You just need to figure him out and help him relax.

I’ve had a very aggressive rabbit as well – he wasn’t mean, just aggressive from what I think was due to fear. Always remember aggression is fear.

I think that giving more room is one of the keys to stopping the aggression – it’s not a cause of it. These aggressive rabbits are extremely smart and they thrive in more space rather than being locked up in a cage that makes them more territorial.

What I used to do with Pepe when he lunged at me was to pet him and tell him what a good boy he was. He didn’t always lunge and bite me but when he did I would pet him.

When I got him initially he was in a 3 story condo and I was afraid of him because he would lunge at me. Pepe was much happier to have free roam of the house and he was an extremely well behaved rabbit – he didn’t chew on anything (of course he did have terrible dental problems).

Here are some articles that helped me with my aggressive buns:

http://www.rabbit.org/faq/sections/aggression.html

http://www.wisconsinhrs.org/Articles/The%20Biting%20Rabbit.htm

http://www.rabbit.org/journal/2-2/mean-rabbit.html

Him marking at your mothers is perfectly normal, as it is a new space. Any change in habitat is going to cause marking, especially since his hormones are still active. Confine him to a smaller area as others have said. The problem is he’s claimed the entire room as “his space” – being cage territorial is normal for some bunnies and you just have to let them out to play with them, but since that room is his “cage” now, you have to get him to switch to a new space.

Regular animal training doesn’t work with buns, they are PREY animals so the training meant for PREDATOR animals doesn’t work the same. Best way to communicate with him is in his own language. Instead of nose tapping him (which is going to make a bun more aggressive, not less usually), or trying to dominate him (which, if he is really a dominant personality, it will just cause a dominance war between you) try talking to him in bunny. If he bites you, squeal and turn your back to him. If he’s nice, pet him and give him a treat (you can break up one treat into many pieces so you don’t over treat and give just tiny pieces throughout the day) or pets. If he’s too persistent, lightly tap the floor with your foot to give the “thump of disapproval”.

Also, if you litter train him at your mothers, he will still mark at home, you need to get him comfortable enough in his own space to stop the territorial marking. Likely that won’t happen until his hormones are all gone, which 3 weeks is not enough time after a neuter to get rid of hormones and often before they go away, there is a spike making the behavior even worse. Patience is key there. Also, when he goes on the floor, what are you using to clean it up? Anything strong smelling may make the marking worse, you want to use just plain white vinegar and water, or something made for eliminating animal smells like Natures Miracle if it is carpet and vinegar doesn’t work.

He sounds like a very scared little bunny to me. I agree with the others, this idea of showing your dominance is not the right way to go about things. I would listen to the suggestions above, it all sounds like good advice.

I don’t think its been mentioned, but I’m sorry if this is a repeat-
Rabbits ARE territorial. He needs to have a space that is his, that isn’t invaded by you ever while he’s in it. Set up an xpen with the door left open even, with all his stuff, hay, water, litter box etc. That is his zone, that you don’t go in, you don’t pull him out of, etc. Clean it when he’s out of it Its what gives them a sense of security and the confidence to build a bond with you.

Its seems crazy in all your research you’ve found stuff that educated you to “bop” your rabbit or try to dominate it like a dog. Rabbits are a prey species, dogs and cats are predators. There are completely different rules You could almost say they are opposite, for example, the alpha dog will groom lower dogs to show acceptance, an alpha bunny *demands* grooms by lower rabbits by putting its head all the way to the floor. Hitting, picking up, holding, etc, that will make a rabbit fearful, not obedient.

4 months is still super young, I wouldn’t worry about him having socialization issues.

Can you explain his setup? Does he have an area the cats/dogs/everyone can’t get to?

Giving him a totally independent set up in an xpen with a hidey box inside it (a willow tent, or my Sammy’s favorite, an upside down big willow basket) provides a safe place for him to retreat to. Under your desk is the same principle in his eyes.

Since he likes it there, I would suggest putting a second litter pan under there as well, in a corner where you’re feet won’t accidentally go into it if that’s possible. He may use it more in a favorite and safe place.

His hormones are definitely still raging. Often a couple of weeks they even get a final surge at about this time and then the final calm down happens after 4 weeks. So wait him out for 2 more weeks at least for that to help.

A bunny will accept you as the dominant animal if you put your hand gently on his shoulders, behind his ears, and press down firmly. He should respond by holding still and crouching down a bit. It’s a spot and position that I’ve heard many shelter workers use to just gain a bit of control and calm in a bunny. Also, your hand is behind his head away from his mouth.

Positive reinforcement. Hidden treats in your hand while your lying down ignoring him, for him to sniff and find. Treats in your pockets. Soft soothing talk to him. Gentle pets where he wants it but don’t push into parts of his body where he doesn’t. It takes time, but he’s already shown you he is safe and comfortable and affectionate with you some of the time, so it’s a matter of degrees and you have much room for hope. He’s a lucky little guy to have you.

Oh, one other point: bunnies love routine. So if you can have a morning ritual (feeding time, play time) and an evening ritual you can stick to, he will like that. It will add to his sense of security in your home.