When I found out that the forum was affected I felt like disaster had hit me. When trying to understand the magnitude I posted this message here.
Rubens answer didn't give me much but a tiny bit and that actually got me thinking more constructive.
FYI I have never had to restore anything with the hosts WHM/CP and didn't really dare to hit the start button.
Then I remembered the config-bak.inc.php and checked the time it was created. It was one second after I hit the button when it all happened.
I also compared the files and then used the config-bak.inc.php as config.inc.php.
Suddenly most things started to work and I dared to restote the header, footer and other affected files. All was within /includes.

I am very grateful for the config-bak.inc.php as it made my day. Thanks guys for building that feature.

After a few days it seem that it works ok.

We can't thank the west coast guys enough for your efforts!!!

Oh I'm a west coast guy too.. but on the Swedish coast and that's a complete different story.
Thanks also to Ruben.