Changing Master Page for Central Admin Site
Today I fixed another messed up thing. The current project that I am working on has 6 master pages for both English and Arabic sites and mostly developed in SharePoint Designer directly with customized theme in the DB ;]. The problem was that the layout and admin pages were still using old blue out of the box layout. I took this decision to fix the stuff so that site looks same. I managed to fix the default and Application.master for layouts and mysite but I faced the interesting problem that the central admin site master page was not accepting the custom navigation and CSS files. But I got the trick while I was reading an article about master pages here and here. I opened my central admin site in SharePoint Designer and edit the master page. I was amazed to see that the master page was using Default.master as its parent so I removed all the custom elements and make it like an normal central admin site which really solved my problem. I know this is not a proper solution but because I am just days away from launch only this is what I can do at this point.