I think the respiratory problems are most likely a myco flare-up. It is common in rats and mice.
When I was trying to get my mouse colony started back in '08, I had a lot of trouble with sick mice. Luckily those days are behind me, but here is a link to one of the threads I made back then. It includes info on dosing the mice with echinacea, to boost their immune system and help them fight off the respiratory problems. http://ball-pythons.net/forums/showthread.php?73792
If you want to use Tetracycline, there is some info in this other thread. I was using it for an intestinal bacteria, but I would guess the dosage would still be appropriate. http://ball-pythons.net/forums/showthread.php?79256
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