Update
The server harddrive developed lots of damaged blocks, this caused the server to crash and has corruped lots of data, luckily most of these corruped data files are system files and not website or database files.
The OS has been booted up in Recovery mode and we are currently tar'ing hda3 (18GB) to a remote location using an ssh tunnel (thanks Sibbi). This will take serveral hours.
Once that is done support will replace and partition a new harddrive with the OS installed. Then we can restore hda3 to the new harddrive, and if all goes well we will be back online tomorrow.