My server crashed due to hard disk errors. While the disk is still partially readable when mounted in a docking station, it is no longer usable. 

The problem is when I try and reinstall Ubuntu Server 12.04 onto a new disk and then restore backups of data and some configuration files via BackupPC I have discovered that the numeric ownerships no longer match thus generating access issues galore.This problem may be due to the fact that the server was initially 8.04, then upgraded to 10.4 and finally 12.4; the new server was a fresh install with users and groups being created in a different order and metapackages being installed in a different order, thus generating different numeric IDs.

While I don't have a complete backup of the system disk, I do have /etc and /home on the backup and access to much of the old system when the bad disk is mounted in a docking station.

Any suggestions for how to get the server up and running quickly and recover files properly?