I know you've been having some litter box issues but what is the litter/bedding you are using?
I'm one of the few (I think, lol) that readily admit rabbits pee stinks! That doesn't mean I don't love my buns, it just means more cleaning.
I scoop out their pee twice a day, sometimes even 3 times a day. Removing it is the best solution, IMO. Once a week I also deep clean with vinegar. My litter is wood stove pellets because I think they absorb the odor very well.
I'm not a huge believer in febreze or odor coverups like those mostly are. I do use febreze a bit but mostly as a refresher and I don't rely on them to control odor. As I said, cleaning and being proactive works best for me.