If you're going to the trouble, why not go an extra mile and do your own heat calc, since none of the contractors apparently did one. Go to HVAC-talk.com, look for blue banner at top of page; click on HVAC-Calc. Will cost you 50 bucks, but well worth it.

I originally had an oversized furnace (125K for 2500 SF). Was noisy, ductwork 'banged', was uncomfortable (hot spots). Since no contractors would do a calc, did my own. Got the right furnace for my home, nice and quiet and comfy.

v

What about installing a 90,000 btu 2 stage, and lowering the blower speed for heat to run on middle and low speed?

Before you can make a choice you need to specify the efficiency of the old and new furnaces. If the old one was 60% efficient then it may have put out 90K BTUH, which as you say, was too much since it short cycled.

You may be just fine with a 70K, 95% AFUE variable speed furnace, but if you stick with 80% AFUE you may need a 90K.

I'd do or get a heat calc performed. I took a look at HVAC-Calc and think I'll get it for my own house to double check the HVAC vendor.

One of them did do a heat calc and recommended a 95% 70k multi speed. I decided I want an 80% so the 90k btu seemed right. However I have 8 six inch, in ground clay ducts, (downflow furnace) and the latest contracor says the blower in the 90k is too much for the ducts. I asked another contractor and he pointed that I have 18 registers, and that the in ground clay ductwork is cold. Hence the solution of turning the blower speed down.