I think the answer to the question of 80% vs 90% is based on info you
should have. Take your last gas bills from a full winter and see how
much you spent on gas. Or better, see how much more you are spending
this year with rates higher and factor that in. Come up with an
estimate of how much you will use per year going forward. Then take
11% of that number. That is about how much you will save with 90% vs
80%. You current furnace may be even less efficient, so you may save
more, but it's a starting point. Now you can figure how many years
it will take to recover the higher cost. In Chicago I think the
coclusion you will come to is that 90% does make sense, provided you
intend to live in that house for a reasonable period.

I also doubt that the cooling problem in an upstairs location is going
to be solved by a new furnace. This is typically a problem with poor
air flow to that area, either supply ducts, returns or both. Did any
of the contractors bother to carefully examine that? That problem can
be very difficult to solve if there is no easy way to add bigger/more
ducts. Did they do a load calc to figure out the correct furnace size?