Okay I found a simple solution unfortunatly it does not chnage the register link but it works. Just kill the register links from showing up at all by using the plugins shortcodes, and widget option.
Widget : Uncheck “Ajax Registration?” option in the widget settings.
Login Page : Create a new page and title it whatever and put this shortcode in [lwa registration = "0"]
Then below the shortcode put Need an account and a button to your own sign up page.
Here is an example of what I have done
http://dev.losethename.com/login/
This version of Login-with-ajax has a modal template and it works very well and looks nice. The options are in Dashbord > Settings > Login-With-Ajax – and there will be an option for changing from divs only – default and modal.
