My guess is that she just doesn't feel comfortable using the WB or she doesn't like the hooded litter trays. I'm guessing that the breeder didn't use WB and although she 'has' used the litter since she's been home, she was in an enclosed area (i.e. the bathroom) and she did have a basic 'pan' style tray.
I would firstly take the hood of the tray and see if that makes a difference. You can buy 'tracking' mats from the larger pet stores to put down around the litter tray so that it doesn't 'track' everywhere. Personally, I'd invest in a little hand held vacuum cleaner...every type of litter we've tried tracks to some degree
Secondly, if that doesn't stop, change your litter, preferably to the one the breeder was using but if you don't know what that was then just try one of the more popular brands in the shops.
As for the comforter you need to give it a good clean with an enzyme cleaning product. Your local pet shop should sell something. We have one here in the UK called Simple Solution which is very effective. It destroys the enzymes in the urine and thus stops it from smelling. If you can eradicate the smell this should help prevent her from toileting there in the future.
Apart from that, it sounds like your doing a wonderful job bringing her out of her shell. I do hope the breeder is genuinely giving up breeding and not just using that as a 'tool' to get you to buy this poor kittens.
No reputable breeder should let a kitten go without it receiving both sets of initial vaccinations and without it being de-worming