@Sheree Hsu If you're pulling permits for the rehab then code enforcement should not be a problem, but I would not go there unless you have to.I would remediate (not test) the mildew or discoloring in her unit and evict her asap.   

When the tenant vacated, the pavers looked like they are now 20 years old, there are stains and it was power washed, but those stains/discoloration are still there.

There are warps in several areas and the siding is discolored.

Purchase a cheap moisture meter and see what the moisture content is on the dis-colored areas and compare to the non dis-colored areas.I have had this problem before when the tenant did not run the AC (trying to save on electric bill) and when buying a house that had beed closed up for a long period of time.Do not use bleach.  

The discolored portion is in a semicircle and is maybe an inch to two inches wide is the countertop usable?

Leaves had stained it and weather had discolored it.

By the time the insurance gott involved it was causing water damage to the interior of the home and was starting to get discolored (we don't use the "M" word in our office.)

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

They expect that the hardwood floors from almost a hundred years ago will be discolored, scuffed, and a little uneven. 

If the stain comes through again or if there is any indication of mold, just replace that piece of sheetrock.The nice thing about sheetrock is that it will usually tell you if it needs to be replaced -- look for stains to come back, sagging, discoloration, etc.