Server Fixed and coming up in minutes
I have fixed the server finally by re-running each world (including nether) through an individual load. It appears that the offender was the netherworld but I ran them all just to make sure. I'm copying the world files back and we should be pretty much good to go after that.
EDIT: Yep it's back up and running fine now. We may have lost anything done in the nether however… sorry about that. Guess I should add that to the backup list.