We will be replacing the ductwork, as well as the subfloor and carpeting in at least one bedroom due to prior pet damage.What was the outcome?

I’m assuming by cosmetic you mean that you are not ripping out walls so you have duct work where you add a condenser, decent electric, Sheetrock or plaster in good shape, plumbing you can keep.

Did you try cleaning out all the duct work?

Has internal ductwork driving their heat but not the AC.

Ductwork looks average, it's that soft padded stuff, not the hard aluminum metal looking stuff.

In doing so, I would have to add a window, door, a little ductwork and a closet that would eat into the square footage of the newly created bedroom?

There is central and and duct work but no AC's, I do HVAC so I figured not a big deal but I factored that in as well.

HVAC is an exception because handling the refrigerant requires a license to buy and handle but many can still run duct work and set up the units.

I will need to redo the duct work and the water supply as there is galvanized steel that has started to develop pinhole leaks.

Depending on how big the house/condo is, split systems can be a good route as it allows for you to skip the duct work.