There is limited discoloration in areas. 

Our contractor is recommended a radiant barrier so that all of the discoloration from the smoke is gone. 

The latter are garbage after, the ply just a little discolored.

We are not talking about Flint MI issues, just the water smells and some discoloring.

Other times, if they are in difficult areas and the flow is good and not badly discolored or washing sediment into the basins, we will only do the main trunk line but leave the subsidiary lines.

That is a lot of mold/discoloration, being wet and in a dark location is the perfect environment for it to grow.

anyone knows what this discoloration on the roof plywood may be?

Structurally the roof is solid, its just an ugly color and some of the shingles are discolored from being under trees.

The walls in the basement seem to have various issues as well (discoloration, chipping).

This is because the entire area where the discoloration is was soaked, and gravity took the upper water down.