I've tried just about every theme switcher plugin out there and seem to be encountering the same issue.
The mobile theme I'm trying to set up is a pared down version of the desktop theme - I'm not including all the pages or functionality of the desktop site. However, the theme switcher appears to work - the mobile theme I select gets loaded - but the header and footer still have the desktop file references for scripts, stylesheets etc that I'm not including in the mobile theme.
Should I expect that this theme switcher will load header.php from both the desktop and mobile themes? Am I misunderstanding how these plugins are supposed to work?