As for the shoutbox problems, that's just how AJAX/Javascript works. You can't call a script from another server than the originating script runs on.
So, if your primary site address is
www.domain.com and you go to domain.com, the AJAX call to update the shoutbox tries to call
www.domain.com anyway. Which won't work.
You either have to only use the main domain, and redirect the other to it. Or possibly modify the shoutbox code so that it calls the same domain as it is running on.
