[Ubuntu Server] - Permissions totally hosed, what to do?

I made some bad decisions when I tried to replace a hard drive in a RAID array on a Ubuntu Server 10.04 system. I saved all of the files, however, the owner of everything was set to root. I have limped along, but there are still problems I keep running into where stuff is messed up because of permissions, file ownership and all my groups are hosed.

I am trying to figure out what to do now. I am thinking I will just backup my home directory, reformat and re-install Ubuntu Server. This seems like the only way to get it fixed. I am just not looking forward to re-configuring things like Samba.

Does anyone else have any others suggestions for a way to recover from this?