However now when I restart the computer it comes up with an Apple Syn Notifier.exe error message about being unable to locate a component because the Core Foundation.dll was not found. I assume this is to do with apple itunes.
That one is actually the MobileMe control panel acting up ... another Apple program that uses Apple Application Support. In
most cases the messages on startup are related to an out of date MobileMe version not working well with a higher version of AAS, but in this case it's probably being produced because AAS isn't actually installed at the moment. To get rid of the messages on startup in the meantime (until we can get AAS installed), uninstalling the MobileMe control panel should do the trick.
Back to the iTunes/AAS/Updates install issues. Could you walk us through what happened when you ran the sfc /scannow? Did the scan go through okay, or did you get an error message instead? If you got an error message, what did it say?