I've actually looked at what they uploaded.....
It looks like they were able to get files onto the server via a buffer overload attack. Checking the logs they were able to run one script which tried to install a spam mailer, but were unsuccessful due to good security practice. The webserver user runs completely without any execute rights so it didn't install properly.
I have also looked at the rest, there was an attempt to grab passwords which was again unsuccessful. I copied the VM to a test network, and ran the scripts as the webserver user. Each attempt failed.
I have pulled down all the files modified after mid-october, and then removed them from the server.
Should be good now guys. There is a security update that vBulletin posted a while back, may have been the attack vector. Will patch things asap.