if you still have the drive you took out, i would put it back in and then reboot.
i know that sounds silly, but i had the same sort of thing happen to my 06 mac pro. it was like the machine wouldn't play nice unless the hard drive buddies were both there. i don't know what the technical issue was, but after i put the removed drive back in, the pro was smiling back at me.
if you have another mac and an external hard drive, if the above doesn't work, i would remove the main drive, put it in the external and see if it's recognized by another mac. just to see if you get the same errors.
hope that helps.
keebler