[dnanian]

I don't know what can or can't be done, because it's quite difficult for me to know what you're definitely telling me. I'd certainly try a clean install and migration from the backup, which should work, but it's hard for me to know whether your trouble with iTunes is due to some kind of mistake you've made, a system problem, the fact that you un-FileVaulted, etc.

I wouldn't touch your backup at all at this time. Let's try, instead, to figure out what's wrong on your real system. When you start up from it, you said the applications are acting as if you were starting them for the first time. What do you mean?