Bummer about the AC stacking issues. It's something I started bringing up about a year and a half ago and it never got addressed.
Multiclassed Characters: I don't have the patched version so I'm speaking of what I know from the unpatched:
You should be able to create multiclassed characters right on the main character creation screen. Example: click barbarian, click add, click druid, click add and now you've got yourself a Barb1/Druid1.
You can't do this method with PrC characters because you need to meet prerequisites before adding PrC levels. So make the character who could take this class, then give him some XP so he levels up, then you can add a level of PrC.
Restoring original files: Other than re-installing, you would want to download and use Davin Church's ET Helper to import and export custom data from the database. You'd have to find someone who hadn't deleted the entry and have them export it and send it to you. This would assume that you had a copy of ET Helper that was updated for eTools 1.2, which I don't believe Davin has released yet. But the whole issue brings up a question: how were you able to delete "core" data?