Its a matter of comfort, not efficiency. The two stage will cycle fewer times and maintain a more even temperature with smaller swings. The variable speed blower will be much less obtrusive in its on/off cycles, ramping up to its run speed and ramping back down. Easier to adjust to the correct CFM for a specific installation as well. The Trane and American Standard furnace/AC are generally the same as are from the same manufacturer although each has some models the other does not. Our AS unit with 2 stage furnace, 2 stage AC and variable speed blower has worked well and uses considerably less electricity than the 10 year old Bryant on the other half of our home.

One thing which might eliminate the need for serious duct revamping, is to have a proper heat calculation (manual J) done. In days of old, most furnaces were oversized. It's quite possible that you could get by with a smaller sized furnace, whether modulating or not. I would question the statement about the gas burner not being able to function due to 'back pressure'. Rather, an undersized duct might not allow the required CFMs to flow, and might be noisy. I went from an oversized 125,000 BTU beast, to a 90,000 BTU Rheem Modulating furnace, which might run in medium to medium-hi speed during mornng setback. I probably could have gotten away with a 75,000 unit, but needed the blower capacity of the 90 for air conditioning. The comfort level is superb. The Rheem modulates in 5% steps, but as BaldLoonie has stated, you would be hard pressed to tell the difference. Most importantly, the Rheem uses a special thermostat to control modulation in a way that the others don't. He has also pointed out other differences between the units. V

Thanks for the comments tigerdunes. We've been over this quite a bit already. The pricing is average for the North East....labor rates tend to be quite high and the $600 rebate makes the price of the furnaces excellent. I obviously have two stage thermostats and the sizes of the furnaces were decided after heat loss calculations. I live in an older home in a cold climate and my calculations were within 10% of my contractor's. The calculation for my two floor unit came in at 75kBTUs. The contractor initially wanted to install a 100kBTU unit, but I talked him down to 80kBTU. The furnace for the renters below me is a bit large, but it was the smallest two stage available from American Standard. I thought about installing a 92% efficient 40kBTU single stage furnace with selectable motor speed, but as the 60kBTU two stage with variable speed motor was the same price after the rebate I went with that one.so that both furnaces essentially the same and to get the variable speed blower. I imagine having the second stage will also be nice on very cold mornings.

Location?...post Mdl numbers...there are 2 major difference between the furnaces...2 stage high eff heat exchanger and the var speed blower motor...I am unaware of any measurable reliability of one furnace over another. I do recommend st steel heat exchanger on both.... While blower motors are very reliable with few failures, the var speed blower mtr model is quite expensive to replace. Just so you know, you can get a 2 stage high eff furnace with fixed speed ECM blower motor, ie not var speed. IMO