In your own custom page you are free to set a different master page. You must do it in OnPreInit event but call base.onpreinit first so that yours is set after the one set by the base page. You probably will need to change the css links as well as the master page.
Look in mojoBasePage and in Default.aspx.cs for example code, not exactly the code you need but it should give the idea.
Best,
Joe