Use 2 units atleast.
Why use a furnace 2 to 3 times the size needed for a small area, when your duct work is already set up for 2 units.
You believe they are sized right. They may be oversized.
Do your own load calc, and see what size each floor takes.
You might find that instead of needing 2 100,000BTU furnaces, that you can use a 60,000BTU on the first floor, and a 80,000 for the second and third floor.
Even old farm houses seldom need 60BTUs output per sq ft for heating.
Try this sizing program, it could save you a lot of money in both installation cost, and operating cost.
Also keep in mind. That newer furnaces require more air flow then older furnaces did.
So if you use the same size as you have now, your duct work could be very noisey with the new furnace trying to move 30% more air.
Same with A/C.