The sentence:
Some estimated that there are 25 assorted insects hanging in the air over every temperate square mile, in a column extending upward for thousands of feet.
(Question #1)
About "over every temperate square mile", which does it modify; "hanging" (i.e. hanging over every temperate square mile) or "the air" (i.e. the air over very temperate square mile)?
(Question #2)
About "in a column extending upward...", which does it modify; "hanging" (i.e. hanging in a column extending upward...", "the air" (i.e. the air in a column extending upward...), or "every temperate square mile" (i.e. every temperate square mile in a column extending upward...)?
As for the first question, I think it modifies "Some estimated that there are 25 assorted insects". IMO we could rephrase it as:
Some estimated that there are 25 assorted insects over every temperate square mile, hanging in the air, in a column extending upward for thousands of feet.
I don't say it's great style, but I think it works.
Regarding question 2, I think "in a column extending upward..." modifies "every temperate square mile" as you suggested.
FRC