You can try soaking the tray in vinegar for 24 hours, then wash out. Vinegar is a great neutralizer. Bunnies love to eat while they poop so maybe that why he ended up going poo in there. (that’s why putting hay in the litterbox is a good idea)
Try buying a few small soft mini-blankets. I usually go to a fabric store and buy couple of yards of soft fleesy fabric, and cut it into a lots of squares. That way, when he does pee or poo in there you can quickly change it to help him get the idea. He will most likely pee and/or poop on it for a while. Many times it’s just to claim it as his own. IF you find that he likes to eat it instead, then take it away. It won’t be good for him to actually eat it.
Regarding his litter box habits: The fact that he’s a baby and using his litterbox at all is wonderful!
Babies and any unaltered bunnies can be more challenging. Babies are especially messy. However, keep training him because though it will take time, he should improve.
The poops that he’s leaving in the bigger penned in area, are they in piles or just scattered everywhere? If he just seems to pile them up in many corners, then get a few litterboxes and put them in the corners. Put poop in them so he gets the idea where to go. You won’t’ have to have a ton of litterboxes forever. You’ll begin taking them out one by one.
If the poops are just scattered, then he’s feeling like it’s his place and he’s claiming it. It’s a rabbit’s way of putting a “white picket fence” around his place, so everyone knows that this is his yard, his house. This will decrease in time as he becomes secure that he has thoroughly made himself clear.
One way to make him feel secure that it’s his place is to only clean up in there when he’s not in there. Since at this age he doesn’t mind being held, maybe someone else can hold him while you clean. In the future picking him up and and putting him back in may make him mark as he may feel like he’s not safe and secure, and hands can reach in and get him. (hence marking, to relay the message, don’t mess with me and my place.)
Don’t be surprised if his habits get worse in a month or so. That’s when the hormones kick in. That will improve once he’s neutered.
I wish there was one simple answer, that if you do it one way, it will all be better. but each bunny really is different and what works for one, may not work for another. We just discover what will work for each bunny through trial and error. So if you don’t see improvement in a couple of weeks, come back and we’ll keep trying until a solution is found.
Keep us updated!