If you do this set the thermostat yourself and put a lock box over it so the tenants can't turn it up too high or down too low.I also like the idea of closing off the duct work to the upstairs apartment and adding electric baseboard heat, this might cost you a few hundred bucks.

In my area, on a house that would sell for that price, you would find the following costs on the things you rung up:Roof: $6kHVAC (units only, I rarely see ductwork having to be torn out): $3-4kWindows (not sure how many times you are replacing windows): $5k for a small houseFloors: $5kSo let's say $20k for everything you listed.

Put all new HVAC in and ran new ductwork throughout the entire house.

And did he inspect the ductwork or just do some wiring? 

All your duct work , electrical, and some plumbing could go up in those runs now.If the house is not a lot of square footage you could do a split AC/Furnace. 

If  $1000, then I would consider split-units or central air if you can get the duct work to fit into your units. 

Brush up on building code requirements: in basements you're looking for egress windows that are 5.7 sq feet or more openable (3ft by 3ft casement style windows work best), and ceiling heights 6ft 8 inches or greater (as little as 6 ft 4 inches is ok under ductwork and beams though)3.

I'll be closing on a triplex soon and 2 of the 3 units share duct work (furnace/ac).

For some houses that are pet free they have new ductwork, never exposed to pet hair, etc. 

My most recent property rehab has all the existing duct in the walls from the old heating system but the furnace and all the ductwork in the basement was stolen.