Moved database (percona mysql) to larger disk, now everything is missing (though the files exist)
Ok, after about a billion headaches I finally figured out what was wrong. Here it is: Some tables are MyISAM and some are InnoDB. I didnt know that when I started, which would have totally helped. So, what ended up happening is that when I moved the files to a temp directory, I guess I messed up the InnoDB tables alignment or whatever you call it, anyway the results where that all the sites that were InnoDB didnt work because I didnt do proper InnoDB moving and it couldnt find those tables. 

So what I eventually realized is that I had been making backups of the database and that I could probably restore the database and get the InnoDB tables back inline where they should be. So what I ended up doing was mounting a new disk at /var/lib/mysql and then restoring the databases from a backup onto the new filesystem that was mounted for /var/lib/mysql. 

Once that was done, I restarted MySQL and it is now running like nothing ever changed. Geesh.. what an adventure!