I recently got a new rabbit, his name is a little up in the air right now but he’s been going by Cedar for a bit. I brought him home and have been attempting to bond him to my older girl who I have had for years, I thought she would benefit from the extra bunny companionship as lately she is only really active at around 2 AM when I’m asleep. She’s a rescue and has always been pretty reserved, I assume she wasn’t socialized very much when she was younger so I thought this might bring her out of her shell a bit.
I started him off with a 4.5 ft by 3.5 ft area because I was told he was already litter trained and that it would be a pretty simple adjustment. I have no idea if I’m doing something wrong or if he’s just slow. He pees everywhere. I halved the area. He is still peeing everywhere. 
I tried a big litter box, I tried a small litter box, I tried a medium litter box. I tried switching to the litter they used at the shelter. I tried keeping it really clean. I tried keeping it pretty dirty. I tried keeping it a little dirty. I tried less litter, I tried more litter, I tried more hay, less hay.
Recently he was primarily peeing next to the litterbox. I thought maybe he was backing up too far and peeing over the edge of the litter box. I moved the x-pen to form a wall on three sides of the litter box and making the space he is in generally a bit smaller. He started peeing in the opposite corner of his space. 
The reason I’m posting is because now I have put another litter box in his space and his space is honestly mostly litter boxes now. I don’t know if this even counts as litter training anymore? I’m at my wit’s end, he is a very sweet boy and I want to help him learn this but I don’t know what I’m doing wrong? I’ve been told litter training rabbits takes only a few weeks usually, I don’t remember my older girl taking this long. And apparently at the rescue he was doing fine?
I’m sorry if this post is too long, I’m really just looking for guidance at this point or some kind of reassurance that I just need to give it time and he’ll figure it out eventually. I don’t like keeping him in such a small space. My other rabbit is free roam so it really hurts my heart to see him so confined, I want him to have more space as soon as possible. 