Have you tried running a hardware test? You shouldn't get beach balls at all while waiting for something. They're not called spinning balls of death for nothing.
Doing a clean reinstall (not just restoring image) seemed to solve similar problems for me in the past; I probably could have debugged exactly what files were messed up, but a fresh install was a whole lot easier. I've had this happen a few times, particularly on systems which were 10.7 and then various 10.7 and 10.8 Developer Previews finally updated to release 10.8.
I'm having a weird problem right now where iMessage doesn't work on an iCloud account for a system which had iMessage installed separately (on what, 10.7? I forget), then upgraded. Presumably the same fix will work.
