That didn't take into account the cooling system, replacing ductwork, OR fixing the issues that may have been found in a flue inspection.

Don't puncture the ductwork. 

The only things that have been completed are the roof/truss, furnace and ductwork, electrical w/ passed inspection and exterior painting.

Then he sprayed coil cleaner on the coils.It more than doubled the air flow, and it was something I could have easily done myself, except that he pulled the unit out of the case in order to reach one side, and I probably wouldn't have risked doing that for fear of damaging duct work or plumbing.The furnace needed a new sequencer and the outside unit got a diagnostic to make sure it was OK.

Then they stole the A/C condensor out of my furnace, busted up the ductwork doing so, took the condensor line to the outside, and took all the important parts of the outside A/C unit (pictures below).

As an example a price guide may say windows are $200 a window you see 18 windows and base your budget off of that but do the windows need aluminum capping or any additional framing. price guide says furnace $1500 but do you need duct work or additional gas lines or vents.

I need to follow up with the AC guy about the ductwork into the new bedroom. 

You can also hire someone to clean the ductwork because a lot of hair can get stuck in there depending on how long the dog occupied the home.Another option is an ozone generator.

Aren't they ductwork chases or something?

So we installed a new furnace to serve unit 1 and modified the ductwork for existing furnace to serve unit 2.