We have done several homes 1300-1500 soft with a completely new furnace & central a/c for $5400-$7000 depending on the extra duct work etc needed for new runs. 

This may involve adding ductwork, installing a separate HVAC unit, or using portable heating and cooling units.Electrical: Another important consideration is the electrical and plumbing systems.

As long as you have ductwork in place, I strongly recommend NOT putting in A/C and instead going with a heat pump.

What neither of them answered was the costs of adding the units; I have done a few flips in the area and have noticed that the bids depend on a few things:1) how big of units do you need (you probably need 2 of the smallest units honestly)2) is the duct work already ready for the units?

The home is so old there is no central air system... furnace would be new, duct work new...

They ran some of the ductwork in the basement, which has an unfinished ceiling, between the floor joists - maybe you could do that?

“Because the $20,000 took so much away from their equity to put into another home, they decided not to sell,” she said.Another client of Chaname had difficulty selling his home because would-be buyers balked at paying $16,000 more for a home with HERO-financed air conditioning, duct work, water heater and insulation when similar homes were selling for less.The buyers argued they were paying for the improvements twice – through the higher valuation on the house and assumption of the loan.

Its likely from all the standing water that it has started to rust out the duct work in the basement or grow mold inside it/throughout it (even on the upper level floors).Saw that recently on a property I looked at with 5 feet of water in the basement from when the sump pump backed up and overflowed (bank turned the electric off 3 years ago).

Since it already has the ductwork, it could be replaced with a forced hot air furnace. 

If you currently have a forced air furnace in the duplex, an a/c unit may not be too expensive, and probably won't require any additional duct work, assuming the furnace is relatively new and a compatible a/c unit is available.