Building code requires you install an ancillary heat source for which most folks use electric resistance baseboards - quite inexpensive and infrequently used.If the building already has ductwork in-place and it can easily be separated, you could consider ducted heat-pumps for each unit (you would not need the baseboard heaters as the ancillary electric resistance heat is located in the air exchanger), but it will likely be cheaper to remove all the ductwork and install ductless units in each apartment.

That didn't take into account the cooling system, replacing ductwork, OR fixing the issues that may have been found in a flue inspection.

.-1-ARUG42C14A Air Handler-1-GSX13042 Condensing Unit (3.5 ton - 13 seer)-Disconnect and remove existing air handler in closet-Install new platform and seal return air chase-Reinstall existing air handler-Repair wiring and reconnect ductwork-Install new refrigerant lines-Remove existing condensing unit-Install new condenser listed above-Reconnect electrical to equipment-Restart system and check operationTotal - $5,450Please let me know if you guys think this is reasonable or if anyone has had experience with this.

Paid about 4K to fix it up which included installing central heat, along with duct work, since it originally had a floor heater.

Think ,insulating, attaching furring to the interior for drywall, limited design parameterers, running ductwork, and mechanicals, asthetics, etc.

The down side of that approach is that it will impact the tenants a great deal due to the new duct work. 

Sometimes the dust builds up in the duct work and of course on top of the ceiling fans where you can't see it.

Kevin,If the furnace (implying forced air) is questionable, why not leverage the existing ductwork and install a heat pump?  

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.

A lot of stuff is included but not installed like 4 new forced air furnaces, ductwork, water heaters, PEX, some drywall, and miscellaneous hardware.