I did the same thing in 2014 so I'm not sure if codes have changed. But I had the same options basically. I ended up just adding a second furnace and duct work. It was not as bad as you'd imagine. But it depends on the layout of your rooms too. I basically just added a bulkhead for the main run crossing the joists. Then it just required small access holes to get runs that went with the joists. A good renovator/furnace installer can really help you out.
I believe the bath fan also has to be tied in to the furnace as does the hood fan. But that may have changed.
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