for sure Blane, those are some mighty valuable files. they amount to an agonizing one page per week.
i find that for heavily formatted docs, i need to clean house sometimes. save another copy to try an experiment. Edit>Select All to grab all the text then hit shift-F9. this will update all internal codes that may be gumming up the works. i do this every so often to correct various codes and references (page codes, footnotes, lists, ToC's). errors that may be there slowing things down will either be automatically corrected, or flagged for you to deal with (F9 will make visible codes disappear again). its worth a try.
good luck on the comps! im sure you'll shine. what's the subject?