Such a nice story in the end.
It usually takes about six months for a chinchilla to properly settle down and trust you. Lots of patience and peace offerings of tasty treats. Sit by the cage as much as you can just talking to her putting you hands up to the outside to let her smell you and stroking her if she doesn't mind (i.e. doesn't bite you). They love to be tickled under the chin. If she does bite 'squeak' in pain so she knows she's hurt you as chinnies also bite to say hello.
If you can sit with your lap by the door so she can come onto your lap in her own time, and again tempt her with treats. You don't want to give too many, but you can cut raisins and other things into small pieces so it feels like more treats.
Try to get some pine in there for her to sit on, she must be uncomfortable, bless her. You've done a good job with the cardboard though. Also see if you can get a sleeping box or hideaway. An old shoebox with a hole in will do for now.
Have a look around the forum for advice on feeding and changing food and make sure she has lots of hay. I'm sure she's much happier with you already. Just have patience and you two will be inseparable soon enough.