Mold is not really a problem when dry---it needs moisture to become active.

I saw a process (On a Mike Holmes show) where mold on the undersides of a roof sheathing was blasted away using CO2. I know our utility uses CO2 to clean high voltage line insulators---no moisture involved.

And water spots are just discoloration, the problem is when the wood degrades.

Wait for the mold test results and research various remediation processes.

Are ceilings stained? If the roof leaked that many places,some leaks had to stain ceilings. You may be looking at condensation damage due to poor atic ventilation which probibly wouldn't stain ceilings.

A lot of old homes have the water stains showing in the attic. Many times the old roofing leaked which was the source of the staining.

Here is a link that might be useful: Bergen County Contractors