How is the music divided? Are there acts or scenes or movements? I'm in the habit of keeping separate Finale files for each potentially independent section of a piece. That way if I add to a section later on I don't have to deal with format issues that sometimes pop up (a habit I developed from using older versions of the program and from dealing with conversions of old files to newer versions of Finale; as a bonus, separated files are smaller and easier to scroll through/work with). I either append the files together at the very end so I can check that my formattings/margins/space between systems are fairly consistent, or I just make separate .pdf files and append those.
Good luck!