The house does have existing metal duct work, but it is original from 1956 .

There are no central AC units, duct work, etc.

It does have a furnace with ductwork.

Thankfully there is ductwork throughout and I personally feel that higher-end apartments need there own HVAC. 

Curious as to what other investors have had to pay for a full HVAC install, new duct work as well.

Do you have a furnace (with duct work) or do you have a boiler (baseboard or radiators), If you have a Furnace adding AC is rather inexpensive).If you have a boiler (which it sounds like you do since you said wall hung unit) you can look into zoning the system, If its not feasible (which it may not be) you can also look into restricting the flow to some areas to balance the systems better. 

.- Complete bathroom, kitchen updateI would like to have a deep understanding of the things to look out for, the considerations to account for such as for example the plumbing pipes, the ductwork, the electrical upgrades, weighing up the different options, envisioning the space.

I have not tried this but an HVAC company suggested UV lights installed in the ductwork or near the AC coil, but I also see stand alone ultraviolet air purifier by googling. 

The duct work (or piping for water-based systems) is very labor intensive/expensive.

Analyze the expense for each of the repairs - ductwork, windows, insullation etc.