Depends on if you will be doing duct work and switching out the existing units or just switching out the existing units?  

., would be offset by needing to redo ductwork, plumbing and opening up walls.

You're gutting it, which I'd think includes replacing all the sheet rock and ductwork, so what are you paying to have 'remediated'?

And 3k for the floor and ductwork?   

Another bad tenant situation.Tenant complains about mice in the duct work.

Adding central heat and Air to a 12 unit could cost a lot of money and be very disruptive to your tenants unless duct work is already running through the walls.

I am currently working on a house that will need new ductwork, furnace, ac etc. 

HVAC ductwork has to be worked in somewhere.

Replaced all duct work when we moved in $1k (we did this)7.

For example, the HVAC unit was replaced 2 years ago along with most of the duct work, there were two pieces of duct work in the back of the crawl space that the inspector noted had light dust and grim on the outside of the duct and suggested it be replaced by a licensed professional.