WHY are you breeding a rat that is possibly sick and stressed? That's just going to put even more stress on her and she will likely just resorb the babies or have a miscarriage from it. Separate her and give her a dose of Children's Benadryl(0.1-0.2mL) every 4-6 hours. Getting them off of those pine pellets was a good thing. It's too dusty for them when it breaks down and pine affects rats more than it affects mice. Their respiratory systems are just too fragile.
Main thing is to get her away from the male so she doesn't end up pregnant. Get her on some low-dust bedding, like the aspen, and try the antihistamines. If she doesn't respond to those, then she'll need to see the vet for some antibiotics.