I wrote an Automator script that handles TC reconnection on reboot etc (save it as an Application and drop it in your Login items) i can post it if your interested when i get home later this week.
I admit I haven't gone back and read all the posts so I'm probably missing something but with my setup I went into System Preferences->Account. I edited my Login Items and just added my TC disk to the startup. When I log in, it mounts my disc on my desktop and I save docs to it all the time. (Granted, I haven't put my iTunes there yet.) But I haven't had any problems and my backups all seem fine as well.