At the risk of sounding foolish, I'll jump in with my opinion. I' m no security expert either, but have learned something about security.
I think your terminology for "rooted" is shall we say "creative".
The fact the all of your files were wiped from the disk, and you seem to have ruled out hardware failure, the logical conclusion is that some process/user with root-level authority deleted all the files. The fact you discovered rootedoor after reinstalling doesn't preclude the possibility that it *was not* there before. I don't know the specifics of your machine and you certainly seem to know what you are doing, and I'm not suggesting you wipe your machine. I don't know if/why any of your clients have root level access, so if they do then it is certainly possible that one of them did it by accident, as you seem to think. I find it unlikely that some arbitrary process did this, and if it did then you need to seriously look at the uids that these processes run as. There is no reason for most programs and I see no reason for any web program to run with root privileges. I am curious though how the re-install was accomplished, seeing as how you live here in the KC Metro and the machine is 1000+ miles away in AZ, IIRC. I'd also like to say, that it appears by your numerous replies on this these threads that you take pretty good care of security, which makes finding out what might have happened more important. Since a successful hack might indicate a zero-day exploit, while it could also be highly likely that a local user's account has been compromised.
Brian