When I was first training my bunny, it took her longer to learn to poop in her litterbox than it did for her to learn about peeing. Like you, I kept her in a smaller space at first, and whenever she pooped anywhere other than her box, I just picked it up and put it back in the litterbox. She got the idea after a week or so, and after that we rarely had an accident.. until.. she hit about 7 months (cue dramatic music). For her, I guess that is when the hormones kicked in. She started scattering poop everywhere, nipping people, destroying everything, and generally being a pain. I got her spayed two weeks ago, and the litterbox habits immediately went back to normal. She also stopped nipping. (However, she is even more hyper and destructive than ever for some reason.) Anyway, it sounds like neutering is a good idea. I’ve heard that some bunnies get the hormonal flood sooner than others. Also, as some others have mentioned, males spray pee once the hormones really get going. Get him neutered before you have to deal with THAT! Good luck!