Document is 500+ pages, so manually pulling apart pages would be a pain. I made a copy of the file and used my own method to split it to single pages, which only took me about half an hour. It just frustrates me that this step now has to be taken, whereas it worked perfectly in CS4. It took me 1.5 hours to troubleshoot the PDF export problem and get to the bottom of it before I decided to just make another copy of the file and break it apart.

If anyone is interested, this is what I did to make a single pages version of my 500 page document with new headers/footers and centered page margins in only 30 minutes:

1. Turned on Layout Adjustment (in the layout menu) as I would be changing margins and I wanted the content to move when I changed them.
2. Changed the document to single rather than facing pages.
3. Changed my margins on my main master page so that the content is centered on the page but the text block is exactly the same width so that no text reflow occurs. I only have a few master pages, because I use text variables to display most of my headers/footers. Also, all of my master pages are based on a main master that controls basic placement of headers and the margins, so I only had to change margins once and the entire document updated (Granted, InDesign crashed the first time I tried to do this!)
4. Redid the header/footers of my master pages so that they display all relevant header/footer information all on a single page rather than across a spread. Since I use text variables to display most of the information in my header/footer, I only had 2 master pages to worry about.

Of course, the inevitable happened. The client came back with a list of last minute changes, and I had to go through BOTH DOCUMENTS and make every change TWICE :-/ Hopefully by the time I have to update this file for 2013-2014 this problem will be fixed so I can go back to just using the same file for both print and PDF!