Okay, so bouncing off my other question this morning, we had one of our team members run "sudo chmod 775 /" by accident. It brought down the entire site..
Once I was able to get in, nginx came up without problems. sshd was fixed with a few changes in permissions.. I was even able to create a new database so at least our site can run, albeit with an empty database..
However, I'm now trying to recover our original database. How can I recover with just ibdata1, log files, and frm files?
http://dev.mysql.com/doc/refman/5.0/en/innodb-backup.html
you just copy them to the right place and start the server, you have all the files you need. If there is a corruption, check the "Forcing InnoDB Recovery" link on that page.