The current system is almost certainly not sized to be compatible with zoning dampers, nor will that actually control the temp in each unit, rather just the amount of airflow.

We've also seen situations where a home has central ac but one room get much colder than others, just the way the air flows through the vents.

An extreme airflow restriction of the return air will cause drainage issues, coil freezing(in severe cases), and poor cooling.

. - If there is an airflow issue in the home (collapsed duct work / dirty filter) it can cause the mechanical systems of the home to provide inefficient comfort (longer run times) while working harder to achieve comfort (higher amp draw). 

Inspectors should have carbon monoxide meters to read any back flow of a chimney, lined or not, if it isn't flowing properly, feeding back gases, get it fixed.Yes, a liner will solve many issues, they lock in place and are fairly air tight to achieve better air flow than an old brick or stone chimney, capped properly at an elevation above the roof line they will solve emissions better than a masonry chimney.

What's the mechanical air flow?

@Matt McGuireBe careful, the filters designed to catch very small particles might restrict airflow that what you've been using, which can throw the system out of balance.

The upstairs has resistance heat - code requires there to be an auxiliary heat source when heat pumps are installed and the unit already had baseboards.Our main level is essentially one big open space with the stairwell to the second level intersecting the middle (there is airflow around both ends of the stair well).  

I also understand retro insulation in walls can be an issue because old houses are not air/water/vapor sealed and require air flow to dry out the framing and prevent rot. 

The basic idea would be a shipping container living space with electricity/insulation/bathroom and some windows to have airflow optional.Thank you for taking the time to do this!