I'm not sure how much customization is possible without rewriting the content server code, but I think you can customize some things - icons, stylesheets, possibly some templates - by overriding the appropriate resources.
See
http://manual.calibre-ebook.com/cust...ates-et-cetera for an explanation. You can find the default content server resources in resources/content_server (the location of the resources folder is platform dependent). To override, you can create a "mirror" of this directory in your Calibre config folder and Calibre will use those resource files instead.
Hopefully that's a start.