Get them off of the pine as it's likely irritating their respiratory tract. Aspen or Yesterday's News would be your best bet and won't stink after a week.

When quarantining a new rat, I never give them a house. It lets them know it's ok to hide from normal things. I only give them a hammock to sleep in and some paper towels to bed down with.

If the sick girl starts acting more distressed, is breating harder, has porph around her eyes and nose, has sunken in sides, or is gasping, you NEED to take her to the vet. The vet will put her on a 7-10 day antibiotic regimen and that will take care of the respiratory infection.