All penetrations for pipes, duct work, wiring or anything else much be caulked with fire retardant material.In many areas a condo separation will require a subdivision plan, with engineering, blue prints and municipal/county review and approval. 

The problem is that I think the smoke has permeated the HVAC duct work as well.

The duct work seems like a big variable so let's say $8k as well.That's $18k in rehab costs before any minor things like flooring / painting / fixtures.Do these numbers seem egregiously off?

It is going to have a rustic look anyway, we are keeping the ductwork exposed, etc. 

I have a bi-yearly contract with them to maintain the units and they currently have a new policy where they check for mold in the duct work by an intrusive method and they are finding slight mold growth and are recommending this device called Nasa Air Scrubber (~$1200 per unit). 

The house has already been completely gutted and framed and has HVAC ductwork, plumbing and subfloors already installed (it's essentially a shell waiting to be finished).

My house was built 100 years ago and has never had central, so no ductwork either. 

New shingle roof - $6-8 per sq ft New high efficiency furnace and all new duct work with 8 reagiters - $5000-7000New high efficiency tankless water heater with new 1" gas line. $3500-5000New hardwood flooring with stain - $10 per sq ft. 

All meters already present, space for furnace already made.This work would include running black pipe, adding ductwork and returns, installing furnaces and AC unit and any other required plumbing. 

We are expanding and also adding a new story to a townhouse in Georgetown and need an investor-friendly HVAC contractor to do all the duct work and install another unit can you recommend a good one with reasonable prices?