First, I would ask the vet to extend their prescription for longer than two weeks. If you are seeing improvement on the meds, that is a good sign, so you need to make sure they get a long enough course of ABs to work through their system. Baytril and doxycycline are the best combination, so stick with that and try to go for three full weeks, if possible.
In terms of their environment, I would switch out the carefresh bedding for polar fleece blankets. Carefresh is probably the best bedding that you can buy at pet stores, but it still creates dust, which is something you want to avoid. Go to your local craft store and buy a few yards of polar fleece (see the scrap bins with clearance prices--often they will have leftovers of fleece for really cheap!). Line the cage with the fleece, and cut up little blankies for them, too. I change mine out every couple of days, and wash them in the washing machine each week. I have been able to reuse them for the longest time now, which has saved me a lot of money over the past 2.5 years!
In terms of their environment, I would switch out the carefresh bedding for polar fleece blankets. Carefresh is probably the best bedding that you can buy at pet stores, but it still creates dust, which is something you want to avoid. Go to your local craft store and buy a few yards of polar fleece (see the scrap bins with clearance prices--often they will have leftovers of fleece for really cheap!). Line the cage with the fleece, and cut up little blankies for them, too. I change mine out every couple of days, and wash them in the washing machine each week. I have been able to reuse them for the longest time now, which has saved me a lot of money over the past 2.5 years!