I would reccomend upgrading to 3.1(5) first and then migrating to a new box - feel free to make a backup of the 3.1(3) system using DiRT prior to the upgrade just in case. 3.1(5) has some updated fixed in the SQLSyncSvr process which DiRT uses heavily on the restore end of things - this is the guy that finds objects in the directory and requests creates when a match is not found and the like so it's kind of critical.
You can't just leave the old box hanging around and do a hot failback... during the restore process the aformentioned SQLSyncSvr service will be "stamping" all the users, locations and distribution lists as being owned by the new server which will render the old one useless - you can't have two Unity servers "sharing" objects in a common directory - any given object has one and only one owner server. Further you'll have duplicate objects (i.e. the all subscribers dl, example admin, default location) in the directory after you install your new box and it can be confusing cleaning things up correctly after wards.
Once you get the new box flying as a new install and it's taking calls and everything's happy, you really want to uninstall the old box and then do the DiRT import. The total downtime is reasonably short this way - if you're not carting messages around (which you wouldn't in your case I don't think) the restore process is pretty fast.
As always, be sure to snag the latest versions of DiRT off www.CiscoUnityTools.com before pulling the trigger - and spend some time with the training videos and read the help file real quick if you haven't already.
