.-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.

If you are talking about installing gas furnaces, then you also will need to be installing forced air ducts everywhere, which potentially means a lot of work (depends on the house) running ductwork.  

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.