The seals in about half the double pane windows were destroyed, and those windows had condensation stains.

As for the HVAC system, to replace a furnace, condenser and coil with a new 2.5 ton unit (probably big enough for a 1200 sf house), I would generally pay $3000-3500.This assumes the ductwork didn't need any repair...

A $3200 install of a $500 condensing unit is a huge markup.

Do not have any return ductwork from the bathroom, as that will pull the moist humid air from the bathroom into the HVAC system and this will be circulated through the ducts; there is risk of this moist air condensing within ductwork and potential for mold to develop.Installing exhaust fan(s) in the bathroom is sometimes a good idea too.

I had this in one of my earlier homes and it was very convenient and reliable.I've actually had a condenser stolen from an occupied unit over a weekend. 

A $300 AC cage i a good investment to protect a $1200 AC condenser.

If you have condensation on the walls, I suggest you use the vent fan or install one to the light, it may not be well vented.

Third person was a HVAC person, put the neutral and ground on the same bar and install a ground rod next to the condenser and attached to the condenser.

I'd rather do maintenance on one central condensing unit than several window units.

Ask the HVAC guy how much it costs to install a new AC condenser or a new furnace.