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. 

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

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

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.

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

You can look at granite, cabinets, tile, laminate, paint, doors, baseboards, vanities, windows, shingles, etc.

The 4-plex and one duplex have asphalt shingle roofs which look like they're approaching the end of their useful life, so I've included enough capex to be able to replace them within 3 years of purchase.

Bathroom showers and tubs - tiled or fiberglass, etc.Flooring - Hardwood, engineered wood, laminate, vinylAppliances - MakeRoof - comp shingles, tile or ?

I will say this, I looked at shingle roofing last night quick as well.

(House was in Highland Park, Los Angeles)Purchase price: $600kRehab: $94k - Full rehab: new layer of shingles on roof, 13 new windows, all new doors, new laminate floors, new 3' front retaining wall, full gut kitchen (new cabinets, quartz countertops, tile backsplash), 2 full gut bathrooms (new tub, floor tiles, wall tiles, vanities, faucets, toilets, vanity lights), converted one closet into a washer/dryer closet, created a master ensuite with a hallway bath, opened up some walls, recessed lights throughout, scraped popcorn ceiling, installed new HVAC, interior paint, exterior paint, stucco repair, new landscaping front and rear of house, new wrap around deck, installed double french doors master bedroom and garage, to new tankless water heater, new exterior lights, updated light plumbing and electrical, new garage door with motor, and some other normal repairs like replacing drywall, floor boards, and replacing some wood trims like facia boards.