3-zone HVAC (HZ432) one zone’s a/c stops working when hot in afternoon

There are a few things you can do which can help:

1) Adjust the dampers in the duct work. Partially close dampers in the ducts going to the first floor and fully open the ones to the second. Take some time to mark them so you know what goes where. It will probably take a few tries to get them set right. That's usually the first thing an HVAC guy will do for this situation.

2) Seal off the leaks in your duct work. Go around and find leaks and seal them with the aluminum backed tape. It's real sticky and has a peal off backing. Oddly enough, duct tape always seems to come loose on my duct work. Go figure. There are services which will come out and blow a smokey substance through your system to locate leaks and seal them.

3) This can be controversial, but you could cover your low returns in the summer and high returns in the winter. The theory is that this will pull more warm air out in the summer and more cold air out in the winter. There are magnetic covers you can get for this purpose like this:

But you may have better luck with stronger magnetic sheets and custom cut them yourself.

I'm not a fan of closing registers, but that's probably one of the simplest things to do.

There are systems that can be installed which will automatically adjust dampers in your duct work based on thermostats placed throughout the house, but they're pricey.

I hope the 90K is the output or it's truly undersized! Even so, it's quite common to oversize furnaces beyond the calculated heat loss by 20-30%. It's also possible the heat loss calculation is low, it's really just an estimate, and part of why the furnaces are oversized. Even if it is undersized, it would not significantly alter your energy costs. Costs are dependent mainly on the home's overall insulation and the furnace efficiency, the capacity and running time is not a big factor.

Changing ductwork will better distribute the heat, but if more heat is leaking out than the furnace can generate, it will not help. While a larger furnace will better heat your home, it will not help your energy costs. If your costs are out of line for your type and size of house in your area, then more heat is being lost than is typical. In the long run, you are better off preventing heat loss than generating more heat.

There are energy consultants in most areas that have the proper tools and equipment to advise you where most of the heat is being lost and what could be done to most effectively reduce heat loss.