Message settings are available at message/edit.php?id=4&course=1 and message/index.php?tab=settings
Concentrate them all at message/edit.php
Create a page called /message/view.php. It should have the usual page header and side bar the same as /user/profile.php It should contain the contents of both the search and contacts tabs from /message/index.php?tab=contacts It should NOT be a popup.
Optionally add a Messages link in the site navigation block. Navigation -> My Profile -> Messages. The Messages link should take you to /message/view.php