I just had a new 3 ton done at one of my homes and had the air handler moved into the attic and some ductwork done, and it cost me $6700 for everything.

Here's what the crawlspace looks like:White efflorescence on about half the concrete foundation blocks, indicating some water intrusionWhite mold in small patches in 1 or 2 spots on the floor joistsA few droppings indicating a mouse or other pest is living thereCondensation dripping off the AC duct work into a small puddle on the vapor barrier, plus one other small standing puddle with no visible source (not a leak, maybe recent heavy rain)I obtained 3 bids from different companies to remove the existing vapor barrier and fully encapsulate the crawl space and install a dehumidifier (2 bids came in at $15k and $16k, one came in for $26k which also included mold remediation and a sump pump and trenching).

They did leave the HVAC ductwork, not sure why, but I had to remove it because it was sooo coated with tar/nicotine that it was not cleanable.  2 companies tried.  

Just to throw in my two cents, something to consider for option 2 is the fact that you would likely need to replace some or all of the ductwork to each of the units.

The fire itself may have been contained to one room, but you will need to look at the ductwork and smoke damage in other areas of the house. 

@Harrison Vann To answer your original question we recently paid $6,700 for complete AC on a total gut rehab, 100% new duct work/vents and AC unit.

Generally you want to take care of things inside the walls first (plumbing, wiring, ductwork, insulation) then drywall/paint, then cabinets/vanities, then flooring and trim.

The basement is partially finished, but the big pieces I need help with are updating a half bath to a full bath (add a shower), turning a dry bar into a wet bar (adding a sink), and moving bit of hvac ductwork.

Im looking at my furnace, and I see which way the air is blowing....based on the direction of the filter AND the fact that the filter air arrows are pointing towards the furnace.BUT...when I follow the ductwork, it looks like the air is getting sucked in from other vents that should have air blowing out of.It looks like this: AIR VENTS <- FURNACE <- FILTER <- DUCT WORK <- AIR VENTSThat makes no logical sense to me.

If I redo the whole roof and duct work for central heat/air.