EDIT: Update is complete!!! Using a dev server to work out most of the bugs proved to be very effective in reducing the actual server down time significantly. We are running on some dev versions of plugins so if you come across anything that is not working correctly please submit a bug report.
I have spent the whole day working to get the server updated using a test server. I have everything as done as possible so it is time to start updating the real server. The server will be whitelisted for probably an hour or so if things go smoothly. I will update this post once the server is back open!!!