Sometimes there are dampers (I think that is what they are called) that can block warm air from going down some legs of the ductwork. 

Any Milwaukee landlords have an idea the cost range of running furnace ductwork to an upper flat?

Some furnaces have the cooling coil inside the furnace, sometimes there is an AC cooling coil installed in the ductwork downstream of the furnace air handler.  

Your talking new HVAC (ductwork?)

I can have an entire system put in, including ductwork, for $5k or so, maybe a little less depending on the setup.

A furnace and central air can be had for a very reasonable price,,,IF duct work doesnt need redone!!

Meth remediation is essentially a full gut job, usually down to the studs and probable removal of the HVAC and all ductwork if this was truly a manufacturing facility and not just smoking.I would encourage you to call these folks and talk to them about what your concerns are.  

You may have to replace the A/C or at lease do a pull and clean on the evaporator coil and blower wheel  then run the ozone generator into the duct-work. 

Find the least obvious route to access the main living floors and cut wall,,,take out all bricks from that side,,,make it into a storage closet type thing and  put new heaters with duct work out sidewalls OR electric heaters with no ducts. 

Dead animal in the walls or the duct work system??