Correct sizing. You need a load calc performed.

I would bet you are oversized especially on furnace. In fact the furnace you are replacing is smaller than the mdl quoted? And just what does that say about the quoting dealer.

And no need to have a two stg furnace unless you plan on a true two stg thermostat. You want the thermostat to control the staging not the furnace
control board.

IMO

I asked about these issues and was told the following; Amana two stage can be controlled by a single stage thermostat (confirmed by Amana that it will call for lower burn for X amount of time before switching to higher burn via DIP switches on control board). Also told that the higher 95% 90K will create similar heat return as the old 80% 100K. We keep our heat settings fairly low as our house is very well insulated. Greatest cost is the heat/humidity removal in the summers.

Wrong advice on furnace size.

Wrong advice on thermostat.

IMO

If your house is very well insulated then that furthers the argument the furnace is over sized. What is the average low temperature in the winter?

You are not going to enjoy the comfort of the 2-stage furnace with the single stage thermostat. Did you ask for a quote to upgrade the thermostat?

Winter average Nov - Feb is 33.9. I will check on the price of a 2 stage. I understand that would require extra wiring.

You are being oversized on furnace and you can't take advantage of a two stg. furnace's capability with a sgl stg thermostat where you would operate off the high stg a large majority of the time whether needed or not.

IMO

OK, help me try to understand something concerning the single stage versus two stage thermostat. Single stage therm with a two stage furnace uses the control board on the furnace to determine when to switch to high; timed based, and according to Amana, an algorithm based on the previous three starts. Two stage therm uses the temperature in the home to determine when to switch to high. So using a two stage therm in a mildly cold morning, as an example, the furnace would be expected to maintain the temp in low longer than a single stage therm as it would switch to high after 10 minutes and stay there until the desired temp was reached on the thermostat? Am I understanding this correctly?