I was keeping (and probably will for the time being, keep) each day's entry in a single file, with internal links to each part. I went through and fixed them so they're unique across all the files, not just withing a single file.
I also have several goals that aren't easy to realize given the traditional file-based view that traditional websites use.
But as others, as well as I (with my Electric King James Bible), have shown, that doesn't need to be the case.
So for the past few hours I've been re-organizing the pages. I have a directory for the year, a directory for each month, and a directory for each day. Within each daily directory I have a file for each section, as well as any other anciliary materials (such as images and what not). Basically, using the Unix filesystem as a database (shut up Mark). I'll have to come up with a URL scheme to isolate the backend processing here, but that shouldn't be that hard.
Basically, this will be an extention of the work I did for the King James Bible. And what I do here will probably help me work out a method to deal with storing and referencing other materials, like Shakespearean plays.