Change featuredPublishers back to the way it was:

var featuredPublishers=["DC Comics","Marvel","Image","IDW Publishing","Dark Horse Comics", "Vertigo"]; /* set to null to disable Featured publisher list */

Then just edit the list.

You set comicsBaseID to true. It's not a true/false, you should set that to 16808. No quotes, just:

var comicsBaseID = 16808;

The featuredPublishers setting shouldn't be true either. That should be an array, like it was originally set. You would then put the list of publishers you want in there instead of what was there. 

The number from the page URL "ie 127.0.0.1/comics/1/ would be 1" is your comicsBaseID. Open settings.js and set that to the appropriate number.

If you have a folder.css and folder.html in your publisher folder (from the last theme), remove that. It's not used anymore.

Console. Ctrl+Shift+I in Chrome. Are there errors in it? I can't help a problem I can't see.

Ok well then is there any error in the console? That's the more important bit.

Be sure to reply to the comment, rather than the thread. Otherwise anyone following is getting notified of these too.

Check if there's any console output (or try clearing your cache). It just not working is really hard to diagnose.

And no, it's not really possible to separate stuff like that. I'm hoping the next Ubooquity might open stuff like that up.

Since we set it up last the settings moved to settings.js. But the function checking for that is the same. Is that it?

I download my header images from comixology.com, or for publishers that aren't on there I modify something from Google Image search.

Ctrl+F5 doesn't necessarily clear local storage, that's why I added this. :)