Sorry about that downtime but I got the server back up and running, although it is still on 1.8.1. If you have upgraded by accident you can read below on how to roll back to 1.8.1. I will upgrade the server to 1.0.0 once Bukkit has a recommended build available (hopefully any day now). If you have any comments, concerns, complaints. Let me know in the comments.
How to rollback to 1.8.1
Windows-Only:
1. Open up the .minecraft folder in appdata (on vista and 7: open up the start menu and type 'run' then press enter. Type %appdata% and press enter. There you should see a .minecraft folder)
2. Go into the .minecraft folder and right click on the bin folder. Click on properties.
3. Go to the Previous Versions tab.
4. Find a version of the folder that existed before you upgraded to 1.0.0.
5. Click Restore.
6. Start Mineshafter Squared and refuse the upgrade option.