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I'd be surprised if they will hurt anyone now, so I wouldn't recommend drawing attention to them ... unless there's folk here who say different! :)
I want to get them out of the site command. Maybe I am not explaining myself :-)
I'm not clear why you are concerned; they seem to be doing no harm, and if they only appear on webmaster searches, there's no lkelihood of visitor confusion.
You say there's no active cloaking going on, just these 'ghost' urls from the past; Why the concern?
You can't use the google URL removal tool if the pages don't bring a 404 when clicked on. That's part of the instructions.
From what you've said, it would take a a fairly persistent, determined and obsessive rival to even find them - though I'm aware such people exist - would they be able to make a federal case out of it? I doubt it.
Even if they try, I've never, ever heard of Google penalizing someone for cleaning up their site - even from people who've dedicated their lives to Google-bashing (such people seem to exist),so I'd really not worry too much. :)