Don’t lose hope! Bonding with shy bunnies takes time, but it is worth it! 2-3 months isn’t too long. 

First of all, stop picking him up unless it is absolutely necessary (like for a nail trim or other medical reason)! Rabbits, as a rule, do not like being picked up, even the ones that tolerate it well. They are “prey” by nature, so anytime they get picked up, they are afraid for their lives. You can add steps or a ramp if you’d like him to be able to go on the bed with you.

As far as peeing on the bed, many bunnies do this because the bed smells so much like human. My bunnies will also pee on anything soft and fluffy, so don’t take it personally. 

The fact that he accepts petting sometimes is a good sign, you just have to respect that sometimes he wants attention, other times no. 

Here are some tried and true tips for bonding with your bun and earning his trust:

– First, and very importantly, be sure that your bun can come out of it’s cage/hutch/pen/condo on it’s own. The pen/condo/hutch should be your bun’s “safe space”. If your bun’s home is elevated, you can use a ramp or steps to allow it to come and go as it pleases. 

-As i mentioned already, only pick him up unless absolutely necessary. Never do this just to spend time with him.

– Once your bun decides to come out to explore, play “hard to get”. ignore them. Lay on the ground while she is out, read a book, etc. If she comes up to you, don’t try to pet her (yet). Be patient and calm around your bunny. Respect if they want to be left alone. “floor time” is seriously one of the best things you can do. 

– Hand feeding! You should feed at least some of his veggies and pellets by hand. You could do this with just the first few leaves of veggies of the day, or a few pellets when you give them.  Fragrant herbs (cilantro, basil, mint, fennel) are all good at enticing shy buns.  You mentioned he eats slowly, but this could be due to the amount. 1/3 cup is a lot for an adult rabbit. My 9 pound monster only gets 1/4 cup split into two portions! Try feeding fewer pellets, and spreading them out over two meals. Talk to him calmly when you feed him so he associates your voice with good things. 

– When he has become comfortable enough with you that he will lay down or relax near you on the ground, you can “ask” him if you can pet him, by placing your hand on the ground in front of him, so your pinky is on the ground and the back of your hand is facing him. If he puts his head down, he wants you to pet his head! If he doesn’t, then don’t force it. Stick to petting only the head and ears until he gets really relaxed with you.  The back and bum are very personal and sensitive areas for rabbits. Sounds like you have made some progress on this already. 

It’s also worth paying attention to whether there is a trigger to thumping or fearful behavior. Perhaps you were spending time with a dog? Or a scary noise in the distance that you cannot hear? 

Hmmm, not sure, but I’m sure he’ll forgive you if he is unhappy with you over your trip. I’ve definitely gotten some scornful foot thumps and dirt flicks (where they kick their back legs out at you) after trimming nails, but they forgive and forget pretty quickly. 

Your relationship with him is relatively new, so you prob just need to give him a little extra attention since you were gone. And maybe have a chat with the pet sitter about whether they noticed any thing weird? 

Bunnies are also super sensitive to smells, so it’s possible you came back smelling different and it triggered some marking.

If it keeps happening, it might be a good idea to make sure there isn’t a health issue going on… is he using his box normally otherwise? Sometimes peeing outside the box can indicate a bladder infection (as can generally grumpy behavior). 

How often do you pick him up to pet him?

You’ve got to put yourself in your bunnies place. Benji may never calm down completely, but that’s really not any fault of yours. As for picking him up, I always try to greet my rabbits before I even try to touch them, I’ve found that if you hold them like a football player cradles the ball they tend to be a bit calmer. Some of mine will actually sit still if I cross my arms under them. I always try to support their hind legs, and I minimize holding them away from my body as much as I can. Oh and even if they are calm and still, I try to get them put down as quick as possible at the first sign that they are getting antsy.
I’ve always been under the mantra that you aren’t loved until a small animal pees on your, because if you really think about it… that’s their way of marking their territory. Sadly it’s also a defense mechanism, I have to remind my niece that she can’t reach directly from the front or the behind but always from the sides so they can see you coming and you don’t startle them.