If we go with High Efficiency Gas furnaces and duct work I can take out two chimneys and greatly improve the layout.

You can get standalone HVAC units for around $2,500 but it all depends on how far you have to run the new ductwork and the amount of man hours it will take to get the job done. 

Is there a way to determine if mold is in the duct work?

My property is a ramber...and when it was time to replace the HVAC system....all I did was in addition to replacing the HVAC, I ran new ductwork through the attic space, then filled in the old ducts with concrete.  

If the ductwork is done wrong, however, there may be little which can be done short of adding booster fans in the ducts.For now (summer), close down the registers on the first floor and force the cold air up to the higher levels.

@Jaysen Medhurst  We are looking to run new ductwork throughout the home but I guess we can always frame a soffit where needed.  

Shortly after, with a different contractor in the same geographic area, I replaced an existing heat pump at my home with a SEER 16 model and completed nominal ductwork for $11,680. 

I need a new unit and duct work done on an investment property.

Paint, water heater, duct work, plumbing, carpet, etc...Can someone let me know if this is good or not?

Once you start opening up walls for electrical and ductwork, you have a can of worms with older homes.