Alright, so I decided it would be good to start over from scratch on my Xbox harddrive (softmodded). I ended up removing the virtual C, then formatting everything.
Unfortunately, I didn't understand the process well enough, and now I get error code 13 when booting the xbox. I tried doing the hot swap trick to load my xbox backup files onto the C: drive, but I still get error code 13.
I also have an EEPROM back up, but I'm not sure what to do with it. Do I just copy the folder onto the harddrive?

Thanks for any help.

To give a little more detail:
I have 5 partitions on the hard drive, 0 - 4
Partition 2 appears to be the C: drive
Partition 4 appears to be the E: drive.
It's a stock xbox harddrive.

Just copying the files onto the drive that were originally on it doesn't seem to fix error code 13. Maybe I'm missing some files?

Try booting Halo 2 and entering X-Box Live (or some other Live compatible game). The game will check your dashboard, and possibly try to repair it.

Don't remove your console from the mains power for too long at a time (if at all). It'll forget the time, switch to error 16, then refuse to boot game discs. Turning the system off is ok, unplugging it is not.

You must be using xplorer360. Partition 3 should be C. What's the softmod package that supplies the files you copied to C drive? You can try Kingroach Ndure 3.1 to generate necessary files.

If you have eeprom.bin, http://forums.xbox-scene.com/index.php?showtopic=244043 will allow you to restore the hdd without having to do hotswapping. Too much of hotswapping isn't healthy for the hdd or your xbox and PC.