He also said the roof was leaking because one shingle needed to be replaced, but that did not explain why every room and bathrooms in the upstairs had water marks running down the walls.

These wood shake roofs are now unlawful in the Peoples Republic of Kalifornia to install, BUT, will a lender lend on a home with an existing wood shake roof that is in servicable condition in a lower risk area, to wit...

So others seem to have assumed asphalt shingles.

At first it was hard to see them because they are mostly black and our shingles are black, but as I looked closer I saw hundreds of the things, mostly on one half of one side of our roof. 

. ;) she had also had the shingle roof replaced, new siding and new replacement windows done before she got sick.   

Are all three pulling their own permits, doing complete year off and new, and quoting the same quality of shingle, same amount of felt/Underlayment, etc?

It's 3 tab shingles not architectural.

Here is how the " rule of 5" would apply on a 45 degree roof with new plywood, architectural shingles, gutters, and tuck-pointing I have to replace.  

About $7k per SFH for me (tear-off, architectural shingles and a ridge vent).

The part that concerns me is the shingles with the caulked edge, if there is no step flashing under the caulk, you are almost guaranteed to have problems when the caulk releases, cracks typically within a few month to a few years depending on the sealant used.