As far as replacing your furnace; I would do it. Furnaces have a 15-20 year life span, at 21 years you got your moneys worth. Also, in the mid 90's a base model would be an 80% efficient furnace most likely. These days 92-95% is considered base madel.
You will absolutley pay more if they come back twice. Additioanlly, older furnaces tend to be larger. So if you replace your AC now, they may have to custom build a box for your A-fram coil to make it fit with your current duct work. Then, if you change the furnace out later and the size is different, they will have to re-work the same duct work that was jsut done. Added $$.
OP, the duct sizing question is very important. Also, be sure they replace the furnace with a smaller one (unless your furnace never turns off when it's 0F or 10F or whatever your design temp is). A furnace is more efficient if it doesn't turn on and off all the time (lower cycle count), and it'll last longer.
Back to the duct question, it seems like new, high efficiency furnaces are designed to have lower back pressure, and suction side pressure drop (compared to 20 years ago). This means you'll want a complete duct redesign anyway (what's the r-value on they ducts, r-8? or r-13?)
which will add a lot to the cost of your HVAC project.
I'm not positive you want to replace the furnace now, but consider going with a smaller BTU output that what you have. Make sure you look at BTU output for a size comparison, not BTU input, because higher efficiency means a 76k BTU input furnace @96% efficiency is now bigger than an old 100k BTU input furnace that's 72% efficient.
Aside: I'm dealing with this pressure drop issue myself right now. New furnaces are rated for a 35-65F temp rise, while old furnaces could cope with 100F+ temp rises ( that's the change in temp from the return to the delivered hot air). But that means you either need to flow a lot more air, or put in a lot less heat. My furnace was way off at 90F temp rise, where the spec says 35-60F. I ended up using the highest fan speed, and also dropping the gas regulator pressure from 3 inches water column to about 2 inches.
This made my furnace a 48k BTU heater, from a 70k BTU heater. The house is still plenty warm, though it warms up a bit slower after we get back from a long trip, and left the thermostat at 45F. I live in Boise, ID, which doesn't get as cold as the midwest, but I'm not in SoCal either. So if you have a 120k BTU input furnace now, get one with 90k input or 70k input. It'll only be 10-20% smaller, but it'll last longer, be cheaper to buy and operate, and keep your house just as warm.