Upgrade OpenPublic to latest release

Hi all,

I have a production site that was built on beta-2, I want to upgrade it to the latest beta but I can't seem to find any helpful documentation on how to go about this process. I followed the usual drupal upgrade process of disabling all modules removing all files and folders except 'sites' and my theme, copied all the new files and folders in to the directory and then running update.php. However after running update.php I can get back in to admin site and navigate around most of it but get time-out errors on other pages like reports and configuration. I can also view some of my content and not others.

I have tried this three times with slight differences but still have the same issue, any advise or link to proper documentation will be much appreciated.