Let me condense this as much as I can...

First, the context - this is a condensed version to give you the general idea. 

You would have a separate air handler in each unit though I do not believe you could connect one condenser to two air handlers.

yep new line-sets, condensers & evaporator coils get very expensive.we have a couple that we're just keeping alive but it's inevitable.

I have the same one in my own house - originally because it blends well with my solar hot water heating system, although now I also take a loop off through a little plate frame heat exchanger to make 'boiler water' to heat my second floor.I didn't like buying the SS stack pipe so my next tankless will be a condensing Navien.

I agree with Curt's advice, approx. 500 sq ft per ton...I also just paid $3,500 for coil/condenser 3 ton unit replacement for a 1,600 sq ft house...The biggest issues you will face with a home that old is running the duct work...If you are not planning on opening the walls, another option is two units, one for each floor so the duct work is only in the attic and basement...A little more costly, so you have to balance out the total costs of opening the walls (or not) if it is not necessary...

I'm in the beginning stages, so I'm trying to condense all of the information out there to must have resources/references everyone needs in the beginning stages.

If you are looking for specifics condensed into one source, "The Book on Rental Property Investing" by Brandon Turner from this site is a great one that walks you through from start to rentals and even common problems you would encounter with tenants in your property.  

But the other day, I drove by and noticed that the a/c condensing unit that sits outside the house is missing.

450 furnace, 500 condenser, 1200 ductwork 150 lineset, 250 coil, 400 misc. total?