Let me guess ..... You installed it with the .tar.gz from the vBulletin homepage, aot a "native" .deb or .rpm from the repository of the server's own distribution ?
I'm probably teaching my grandmother to suck eggs here, but it's always best to use distro-specific packages when you can cos they generally are patched to Just Work pretty seamlessly -- often with a post-installation script that takes care of any changes to file formats / database schemas by backing up the existing data and auto-converting it. Of course, all that depends on someone actually having done the hard work in the first place; and I don't even know what distro is underneath this. If it's not something very popular, it may well not evrn have a "native" version of vBulletin packaged for it. (I started out with Mandrake, before it became Mandriva. Lovely to look at, delightful GUI setup tools, but kind of short on native .rpms. Painful memories of learning the hard way about building from Source and what *-devel .rpms are for .....)
The warnings about deprecations look as though they are from PHP 5.4 -- I had a 'mare myself trying to update some scripts written in-house by my boss, my predecessor and me up to 10 years ago and relying on old pre-4.2 behaviour such as register_globals and magic_quotes, which has been removed altogether from 5.4. All of which had to be done in less time than we originally planned, due to the old server exiting stage left for the Great Data Centre in the Sky .....
Actually, for my last major web-driven project, I wrote the whole lot in Perl just so I didn't have to bother with PHP.
Oh, and one final tip for any aspiring boxherds: Avoid hardware RAID controllers! If you use the Linux kernel "md" software RAID drivers, each individual drive looks exactly as though it was just a normal drive on its own; you can just take the good drive, plug it into another machine with a cheap-as-chips USB-SATA drive enclosure and mount it ..... The 3Ware RAID controller in that old server must have done some weird stuff with the low-level formatting, because its disks were not readable that way ..... Only another 3Ware controller could read them.