I'm not sure what type of set up you have for your bunny, but I take it he's indoors ? Does he have a designated place to wee and poo, such as a littler tray ? Quite a few of us use those large plastic underbed storage boxes, as they are shallow enough for a bunny to jump in and out of easily, and are relatively cheap. A few sheets of newspaper with hay on top, placed inside, encourages buns to sit and chew and poo and wee at the same time, which they seem to like doing :? Just a thought, but hope you get the stains sorted anyway x