If you were updating from the most recent RC, you shouldn't see a whole lot when you run update.php anyways. I'm not even sure there are any... maybe for one special case. Also, if you left the old Ubercart directory in a modules directory and simply renamed it, Drupal will still find the modules inside of it and cause the conflict you're seeing. If I were you, I'd zip up a backup of your old Ubercart directory (or download it to a local computer) and remove the directory entirely.

Be careful that you don't wipe any contributed modules you were using... you might also check through the release notes to make sure you're not going to lose any functionality.