I'm not a professional and not living in the US.

1. Get a Wood Moisture Meter and check everything. If the wood contains more water than it should you have an ongoing problem and there is ongoing microbiological growth.
2. Some of the Black / Dark parts look like fungus. (In Swedish "svartmögel" which is directly translated to "black mould"). That shit can cause allergies and worse shit.

All in all: get a professional to check this. I'm Sweden we have "building inspectors" that are experts in leakage and mold that checks this for you.