I think what helped me a lot was white vinegar solution. When you put Ziggy inside his pen tonight, spray white vinegar solution liberally to all the areas where he pooped and peed. Let it stay like that over night. Clean it next morning. Hopefully some of the odour of his pee and poop might have gone by then.
From my personal experience I can say that rabbits dont poop and pee everywhere, they have certain 4-5 places which they mark and recognize by the smell or their pee and pellets. Next you can follow the usual procedure..setting up the litter box where you want to, putting their poop and tissue soaked in his pee inside the litter box..when they use the litter box, giving them a treat and a pet (treat is more effective than pat ^^;; )
My bunny Moshu isnt yet perfectly litter trained but white vinegar solution and treats helped me in achieving whatever we have, in a matter of two days.
The key idea is to remove the existing smell from the areas where you dont want her to pee and poop and to guide her to the litter box, hence you drop some of her poop and pee in it.