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.

HVAC issues-- not just the furnace/boiler but also the duct work design and materials. 

After some deliberation, I decided to let it go and let them get away with February for free in addition to all the months they'd been owing before that.Now that the deal had closed, I gave her a choice on the heat: either have handymen busting up the floors and ceilings for a couple weeks to lay new duct work, or install new electric heating.

In my estimation to do a tap in and run the lines + add two furnaces + ductwork is going to cost around $9,000.

I am just afraid that if I need to put a new roof on and new wiring and install an Ac system and Duct work that it’s not going to leave much for everything else.

However, I continue to find more pieces of insulation appearing in the ductwork several months later. 

Major duct work is needed and yah knew that.