Sorry for the delay, we where putting our Cub Scout career arrows together for their crossover ceremony on Monday.
If I was doing the upgrade, I'd put the new files on the server, then overwrite the files on the server with your old includes directory, the styles/wrapper.inc.php file, and the /cache_builders/custom directory; then run the upgrade script on the old database (be sure that the same working connection data is in your includes/config.inc.php file).
