As part of vBulletin 4.1, Freddie has been working on an overhauled upgrade process.
It enables upgrades to be performed seamlessly from vBulletin version 3.5.4+
The upgrade can be run from command line as well, in case your board is sufficiently large that the upgrade process times out in your browser window.
(sorry in advance for the poor audio - I did it off my laptops inbuilt microphone)