I am not entirely sure, but at the very least I can give you the changes for the navbar that made it so it could be logged out. (very simple and small, changed from a button to a text link)
What I would do when installing a style and customizing it (and this is from working with styles for a long, long time) is to make a child style of the custom style and work on it from there. So you always have the root custom style that is an easy upgrade.
BTW, Edog! Does your site still have issues with the ajax menu for reputation? You are the only one to mention this to me and it works fine on my live version.