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I don't think sitewide links are a good idea any more.  Im sure they have been legitimately placed but in the eyes of a computer could look like paid links  which as we all know is a bad thing.

My advice would be contact each website in turn and ask for an editorial link rather than a sidebar/sitewide link.  This way you keep a genuine link.

If they refuse then I would ask for it to be removed as in my opinion these links are more than likely the cause of your penalty despite them being relevant as if they link to your fan site they are probably linking to lots of fan sites so could also look like a link ring of some sort.

The problem with sitewide links and sidebar links is that they have been abused by the spamming world so stick out as if a paid link despite in a lot of cases actually being genuine.

You have got to remember that at the end of the day it is a computer analysing these links and they are not quite there yet.  Although they are legitimate there are hundreds of thousands that are not and this im guessing is what Google is basing it on.

I would go with the brand name of the website as well.  Just ensure you have great navigation to filter any strength through to the more targeted pages and start producing content on these that is linkable also.