Think I have at least worked out what the injection does.
The <?php eval(base64_decode <insert value here>
contains an address to a folder in the installation.
In my case it was a theme helios multi template.
From 28th of April, until now, 25mb of files was stored there.
Over 2100 files.
All of which seems to be links to other infected sites which has been injected with commercials. With several commercials in each.
Many of the commercials seems to be flash files, which I haven't tested to run yet, but I downloaded all the files that the hack left and I'm going to inspect those closely.
Not that I will be able to make a difference in sorting out how to fix it, unless you can run a preg_replace and remove <? from files uploaded. But I'm not there yet with my php knowledge, so I'll just continue researching and posting what I find.