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You are right about the registry - it is a nasty beast at the best of times!
Now I don't really know the correct procedure to get you out of this fix, but you could try a utility program such as Norton or Nuts' n' Bolts. These programs scan the registry and find stuff that's no longer needed etc etc, but they don't always get it 100% right. However they have some pretty decent registry editors..
I think you are right in tracing references to the files outlined in the registry and deleteing them, or literally deleting everything every refernce to the software that was allegedly un-installed.
Alternatively, what about a complete re-installation of Windows? You can install Windows without re-formatting the drive.
Sorry I can't help ya out more.
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