It sounds like your bunny has built habits that are going to take some effort and time to break. Out of curiosity, how long ago was he neutered?
Also, do you have any other pets?
How much freedom does he have right now?
– My suggestion is to limit freedom to the size of an xpen. And of course during training, put down things that you can wash up easily.
– As soon as you notice he’s gone in the wrong place, get a paper towel clean up the urine and poop, and put a piece of the urine soaked paper towel into the box along with some of his poops.
– Then clean up the residual urine and poop on the flloor with a solution of 50/50 water & white vinegar. Sometimes if you use other scented cleaners, it will make a bunny mark over the perfume kind.
– Get a few litterboxes, add hay and bury in a few healthy treats, like rosemary and mint.
– Spend 20 minutes a day focusing him on actually litter training him.
During the 20 minutes:
-Get in the x-pen or be in the room with him watching him closely through his cage (whatever set-up you have) Best time to do it is when he eats, because many bunnies will poop and pee when they eat.
-The best way is to catch him in the act, and at the very moment he begins to lift up his tail then scoot him to the box.
-Try not to pick him up and put him in there, but if he won’t go on his own, then just put the front part of his body in there and touch him on his backside to encourage him to get all the way in. Allowing him to get in will make it better for him to learn. (all the while, saying the word litterbox),
-Then give him a treat OR if he seems threatened or bothered while in there and/or jumps out if you approach him while he’s in the box, then it’s best to back away completely so he feels safe in there.
-During all the other times that he is not peeing and pooing during your training session, then use that time to teach him what the word "litterbox" means. So every few minutes start saying the word "litterbox" and guide him to the box.
If you do this everyday, then I would say in a few weeks, he will jump into that box on his own, so if you start to see him lift his tail up, you can repeat the word "litterbox" a few times, and he should jump in.
All of this may take even more time though as he is a bunny that was never used to using a litterbox. So be prepared to do this training everyday for several months.
Good Luck and keep us updated!