There are drugs to treat aspergillus, German Shepherds are actually predisposed the infections. They are one of the breeds that get the fungus in the nose. There is a blood test to determine if that is the culprit. For inhalation of most molds, air flitration and elimination of the spores is needed. You might consult with the local public health authority. Most counties have an employed doctor to help with these problems. This sounds like a problem that needs specialist consultations.
For problems that are over my head as a general practitioner, I usually consult with veterinary school doctors or other specialists because I have found it takes several minds to solve some problems.
In some places there are people that will come into your house and inspect for toxic mold in the walls.