I'm spending about $5K to replace the AC, furnace and duct work.  

Of course, an experienced contractor would bring this issue to you in advance and resolve it but he overlooked the fact where a ductwork for a central air is not feasible.

If not, have insulation contractor spray several inches of cellulose. 2) be sure the duct work is not leaking air.

Now you could keep 1 boiler and put in a coil in the ductwork and use it as emergency heat . 

James Park,You will be able to deduct as an expense anything that is replacing the property back to the condition it was in before the damage occured with the exception of structural components that must be depreciated such as: furnace, duct work, structured support, essential wiring.

Consider calling your HVAC specialist and have them inspect the coils and ductwork of your cooling unit.

There was no central heating and cooling, so I added it complete with new duct work.

Only to receive and email from my lender stating the underwriter may not be able to finance the deal due to the fact there is only one furnace, one A/C unit and one set of duct work. 

I have them in one rental and know they are more common in some new builds in some areas as you don't need the duct work. 

The duct work was already in place so All I had to do was install a furnace and run a new gas line and have the project inspected.