Give him time. It can take a month or more for the hormones to decrease much.
Also, try to prevent him from playing with his litterbox. Usesome sort of clip to attach it to the cage wall or put a flat weight inthe bottom so it's too heavy for him to move or flip.
Does he have much for toys? And does he get much exerciseoutside of his cage? He might be playing with the litterboxbecause he's bored and has too much pent-up energy. If helikes big things, give him a cardboard box or untreated wicker basketinstead.
I also agree with Bunnys_rule's suggestions about keeping the food nearthe litterbox. Put the hay in the litterbox or in a rackabove it and put the food bowl next to it. Lots of rabbitslike to eat and poop at the same time, so if his food is in/near thelitterbox he'll poop there.
Also, clean up any urine stains with vinegar. Otherwise he'llsmell it and think that it's the right place to pee again.