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.
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.
