I'm currently playing around trying to customize the Share UI. I've found I'm able to do so by modifying the template files for the UI. For example, editing this file and restarting Share's services:
C:/Alfresco/tomcat/webapps/share/WEB-INF/classes/alfresco/site-webscripts/org/alfresco/components/header/header.get.html.ftl
However, is this the optimal way for customizing the UI? I get the desired results if I edit this file, but I know when upgrades come, that I'd have to merge my edits with whatever edits are in the update file.
Edit: Also, to be a little more clear. I'm trying to customize the way the header and toolbar looks. This includes removing certain items (Sites, More) and making a few other tweaks. I'll also want to make tweaks to other parts of the UI, but I'm starting with the header to see what I can do.