I practically did the same thing as you did. Moved to a new server and update to the latest OTRS version, at that time 3.3.3. Worst part was, moving from a Windows server to a CentOS server (the bad part was getting rid of all Windows specific stuff in the config files).

If you move to a CentOS (6.5) server, I can give you a small part of my own upgrade documentation, with which you can easily install/update the AddOns on the server directly using the “otrs.PackageManager.pl”, kind of a checklist thing. (would also work with RHEL 6.5)

Consider donating the whole document to the project. Enough people do this that it’d be a valuable addition to the project documentation