There have been no leaks but shingles go missing when a big storm comes through and they have to be replaced.  

Also need to mortar around at least one window and seal it up, as well as replace several shingles on the roof.

It wasn't bad with one house, I would not want to go through it again for a lot of houses at once, especially with the T-Lock shingle issues that are coming up now.

Rehab included granite in kitchen, upgrades in ceramic tile, new cabinets, create a informal dining space in kitchen with granite bar, all new window, architectural shingles, upgraded vanities, etc.  

Once removed you'll need to replace the plywood and shingles on your roof, drywall the hole in the ceiling, build up new subfloor, and finally patch the flooring you have currently. 

Cheaper and lasts 50 years when shingles only last 15. ~$5k) Needs every wall painted and every floor re-done.

I would recommend you ask your home inspector to be sure you don't have that issue.Other than that some bigger price tag items you want to keep in mind.  1- The roof- When was the last time it was replaced or re-shingled and how long do they last in your area. 

Have a roofer that installs slate roof look at it, that is a specialty and not every roofing company does it. some just want to install asphalt shingles, quick easy money for them. when i see slate i see quality material, I am a contractor and just like @Chris Seveney said, i would take slate any day of the week, but you need to find out if it needs repair and what it will run you.

So hypothetically, if the roofer says rip off and replace all the shingles, for example, how do I propose to restructure the deal? 

Other parts of the roof (lower) are newer shingles and in good condition, another rookie mistake was I didn’t ask how old the roof was and just assumed about 10 or so years.