If the latter, you have to get ductwork into place and that adds to the cost. 

The particular project was a 200+ year old historical property and modifying the ceiling or wall framing for ductwork was going to be impossible as we were using a lot of exposed framing as interior finishes.

Areas are different, but here I can get a new HVAC system, all electric, with duct work for 1,000sf for $4k, from a small, licensed AC guy.

He ran all the duct work & out the door, we paid $4600, which was an absolute steal.

Can anyone recommend a company that can clean ductwork at a reasonable price in metro Detroit?

They allow you to finance certain capital expenses like roofs, HVAC, duct work, insulation, solar, etc.

Here is what I would do: block off the duct work to the "extra" bedrooms.

And it may end up being cheaper (relatively) to just remove the top of the roof and put in new trusses, joists, insulation, duct work and reroof.

@Brian Kloft I have the heaters you mentioned as well as heat pumps with duct work.

It also looks like that wall floats, so you are probably going to have some stuff in the soffits above the cabinets - at a minimum, ductwork for the range hood (if it's not vented back to the room) and possibly electrical wiring.