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I've checked all logs and cannot find anything out of the ordinary. The only thing I did was install mod-security (and then removed it via apt-get remove after I was getting errors). Now the site cannot be connected to at all.
I've also restarted the VPS just to check that and disabled all add ons.
I've checked all the config files for modification dates for Apache, php5 and mysql but none are recent. Any suggestions where to look since xenForo apparently doesn't write an error file that you can use.