One thing that can cause issues is having bedding throughout the cage. It can make litter training confusing for them. I would suggest taking the bedding out. You can try putting fleece fabric or newspaper down instead, but sometimes that can lead to accidents too. But you can try it and see how your rabbit does. Just keep an eye on if your rabbit tries ingesting any of it. Also try a larger rectangular litter box, then you want to put the hay rack so that your rabbit has to sit in the litter box to eat the hay, or you can put a pile of hay in a corner of the litter box, preferably a corner not usually peed on. The idea is that rabbits poop while they eat, so if you keep their hay where they have to sit in the litter box while they eat it, then the majority of their poop will stay in the litter box. You may also need to put a layer of hay over the litter, as some rabbits won't want to use their litter box because they don't like the feel of the pelleted litter on their feet.
For the rectangular litter box, you can use a cat one or a plastic storage bin, just whatever will work for you and fit in the space you want it in. You just want it big enough that your rabbit can move around in it comfortably and eat. One thing with the hay rack too. You just will want to make sure that it isn't too difficult for your rabbit to get it's hay through the cage bars, or it may discourage hay eating.
A rabbit is really considered litter box trained if it consistently pees in the litter box. Poop is a whole different matter. But some of these tricks can help keep the poop more confined to the litter box. Also neutering, when he is old enough, often helps.
