I plan on making more than one paper mini for the Jam, and I find it's usually easier to create an individual sheet with multiple copies of the same character (since I usually make stuff for wargaming, where it's better to print off five of the same model at a time than one of five models). Is there a limit to how many pages our submitted file takes up, or can we use as many pages as we like?

There is no limit whatsoever! You can submit a miniature pack with all minis on 1 paper or several copy of 1 mini per page. And you can submit multiple packs as well so that you can divide them as you want.