So far, we have not identified mold in the house...it is believed to be in the crawlspace, mainly around the existing ductwork (old and uninsulated) that will be ripped out during the project.

Kilz in subfloors, if it soaked that far, but I am always a fan of replacing where needed, since MDF is pretty cheap.Then if you aren't replacing ductwork and HVAC, then get those cleaned and serviced.  

I wouldn't do anything about duct work unless there is evidence of the insulation flaking, then it should be addressed.

I bought a hoarder house at about 30% of market value and had to fully renovate it plus deal with hauling off junk, cleaning, removing trees, cleaning up the yard, replacing the furnace and all duct work, etc.

It needs an AC and duct work.

This may involve adding ductwork, installing a separate HVAC unit, or using portable heating and cooling units.5.

In northern climates, unless your attic is part of the conditioned living space, placing your furnace or even ductwork there is not a good plan.As Pat mentioned, your utility bill will be higher as the furnace will need to work harder to get heat to the living space as it will be heating the attic as well.

Whether central air in a hot environment or a heating system in a cold environment, you most certainly can seal all penetrations {in practice, we've encountered very few contractors who seem able to do this}, insulate the ductwork and leave the mechanical unit to function in a space that is sufficiently warmer or cooler than the conditioned space to impact its performance. 

Expenses included: plumbing, duct work, electrical, and lumber. 

The law specifically states:"Sleeping units or dwelling units in I and R-1 occupancies and R-2 college dormitories, hotel, and DSHS licensed boarding home and residential treatment facility occupancies which do not themselves contain a fuel-burning appliance or a fuelburning fireplace, or have an attached garage, need not be provided with carbon monoxide alarms, provided that (a) The sleeping unit or dwelling unit is not adjacent to any room which contains a fuel-burning appliance, a fuel-burning fireplace, or an attached garage; and (b) the sleeping unit or dwelling unit is not connected by duct work or ventilation shafts with a supply or return register in the same room to any room containing a fuel-burning appliance, a fuel-burning fireplace, or an attached garage; and (c) The building is provided with a common area carbon monoxide detection system."