You will also want your ductwork cleaned, along with the airhandler, and filters replaced.If cleaning doesn't solve it, and you still have some residual odors- Deodorize using product specifically designed to eliminate (not mask) odors.

Paid about 4K to fix it up which included installing central heat, along with duct work, since it originally had a floor heater.

Think ,insulating, attaching furring to the interior for drywall, limited design parameterers, running ductwork, and mechanicals, asthetics, etc.

The down side of that approach is that it will impact the tenants a great deal due to the new duct work. 

Sometimes the dust builds up in the duct work and of course on top of the ceiling fans where you can't see it.

Kevin,If the furnace (implying forced air) is questionable, why not leverage the existing ductwork and install a heat pump?  

In my area, on a house that would sell for that price, you would find the following costs on the things you rung up:Roof: $6kHVAC (units only, I rarely see ductwork having to be torn out): $3-4kWindows (not sure how many times you are replacing windows): $5k for a small houseFloors: $5kSo let's say $20k for everything you listed.

A lot of stuff is included but not installed like 4 new forced air furnaces, ductwork, water heaters, PEX, some drywall, and miscellaneous hardware.

asbestos on pipe or duct work in the walls - undisputed is fine.

Now, getting ductwork allergen free is another thing to include :)