However, since this is a remove and replace situation, will any of the
points you mention really apply? The house is prefectly comfortable as
is right now, it's just that the existing furnace is 35 years old.

The reason why I posted this question is that the comments I've read
about the installation being most important are usually part of answers
to persons just like me ... replacing a furnace, not a brand new
installation. I can understand a brand new installation where all the
duct work needs to be run, etc. That's a lot more planning and more
chance of things going wrong like you mention. But what can go wrong
when you're basically swapping in a newer furnace.

Thanks,
Harry