A double furnace install is common in Calgary and most builders oversize on new homes here so people don't complain of being cold. It has been known to get to -45*C in the winter here.... Recently.
If you put 2 45's in I doubt they'll shut off ever, when we get those cold snaps.
I agree the 90 is too big, I would look at something in the 60-70mbtu range for the main and a 45 for the top floor. 2 stage and ECM for sure.
A 2 stage 70 will start at 40-44,000btu on low fire to keep your costs down and you'll have that extra capacity when needed.
Make sure they run enough wires so you can actually control the 2nd stage!