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Thank you so much for all your hard work! I am not currently using VF, but I still like to follow its development.
Do you have a link to your site?
Have you take a look at the Vanilla 2 Upgrading Tips post?
Try re-uploading the files again and then visit /utility/update. You may run this more than once.
Do you have RewriteUrls enabled for_ 'pretty'_ URLs by any chance? That's could be a reason for that not working. Copy the 'RewriteUrls' setting from config-defaults.php into your config.php file and set it to true. Then try again.
Try deleting the .ini files in /cache.