I had one apartment that was so bad I had to replace the HVAC ductwork, the HVAC, the carpet, the ceiling tiles and repaint all the surfaces, plus put in an ozone machine for several days!

If the duct work is all already there and ran for all three units.

For asbestos wrap around duct work, we encapsulate it with paint and then build a chase around it or have it removed. 

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.

Don't puncture the ductwork. 

The only things that have been completed are the roof/truss, furnace and ductwork, electrical w/ passed inspection and exterior painting.

Then he sprayed coil cleaner on the coils.It more than doubled the air flow, and it was something I could have easily done myself, except that he pulled the unit out of the case in order to reach one side, and I probably wouldn't have risked doing that for fear of damaging duct work or plumbing.The furnace needed a new sequencer and the outside unit got a diagnostic to make sure it was OK.

Then they stole the A/C condensor out of my furnace, busted up the ductwork doing so, took the condensor line to the outside, and took all the important parts of the outside A/C unit (pictures below).

As an example a price guide may say windows are $200 a window you see 18 windows and base your budget off of that but do the windows need aluminum capping or any additional framing. price guide says furnace $1500 but do you need duct work or additional gas lines or vents.