By home system, I mean the files that I upload to the site from here. Since you did the upgrade, I didn't actually have any of the new files.
I downloaded all directories from the site yesterday and overwrote my existing files, added the new ones, deleted local ones that no longer existed on the web server. Since they came from the site, don't think it'd do any good to re-upload them again.
Not sure about how to proceed with files in the root since I know some are customized and I can't remember which ones. ...
PhotoPost Pro 8.23, Shared Host, Linux 2.6.27-grsec4, Apache 2.2.11, PHP 5.3, MySQL 5.1.85, GD 2.0.28,