Rawspice: What you have to know is the mold you are dealing with is not just located on the outside of your ceilings. It is behind there and probably embedded in the rafters, as well. Your carpet may be part of the culprit, but you seriously need to get someone into your attic to investigate and see how widespread the mold growth is up there. Just cleaning the spots on the ceiling is only touching a very small part of the mold growth on the other side. No matter the type of black mold, the spores and even the vapors off that growth can cause you all the trouble you describe; and, over time the symptoms/damage can become permanent, even if you get rid of the mold entirely.
Good Luck!!