There are so many factors that random people on the internet are not really a source of information for your exact case.

For instance: You didn't even say where you live. A/C needs in Philly are very different from those in Florida or Los Angeles or Chicago. No information on type of construction, amount of insulation, attics, type of A/C (ducted or split), sun load, etc.

Call some local contractors tomorrow. You and they have a lot of work to do.

Generally speaking, doing separate "zones" is a good idea, but whether your ductwork can support that or not plus the expensive of it could be limiting. In the south where I am, zones are a must. Multi-level homes are especially difficult to control heating and cooling, so you do need a professional. Rather than someone who sells and installs said systems, I would get a HVAC "consultant" who isn't in the business of "selling stuff", but rather will give you a good technical assessment of what best practices are and feasibility of same. Not an easy project for sure! Messy too.

Thanks. The place currently has three separate units, but very old.

I now know more about HVAC systems than I could have ever imagined! But the time invested in research paid off! Our bids ranged from the low end of just under $14K to over $30K.

Make sure you get a REAL load calc. But you can also do a pretty good estimate of your own. Read hvac-talk.com for the info on using your electric and/or gas bills, and check your current system for run time to see if it's over sized. (Our old one was 2x the size we needed!)

And the most important thing is the quality of the installation. (If you are in the Minneapolis area, I would not hesitate to recommend the company we used.)

It sometimes depends on the exact configuration -- how many returns, how much the floors are open to each other, and the like. I'm currently doing an older house on this approximate scale (three levels but a bit less sf), and my HVAC guy insisted on at least two units. If you already have the ducts and blowers, then you should probably do the same.

Flo Mangan - would that be a private energy consultant? I'm asking because, the one we paid for through our utility company was pretty much worthless. Honestly, just another government sponsored "check the box" program. Didn't tell us anything we didn't already know. A complete waste of time and money! (I'm sure there are some good ones - somewhere.)