g1smd - 12:21 pm on Sep 10, 2012 (gmt 0)

It's almost as if Google is using historical versions of our pages to visit historical links to presently non existent pages, and then giving errors for it.

They do, and they need to ask for the page that links to the page that links to the page and confirm 404 all the way back up the chain before the data in WMT will change. This can take many months. As long as the list of 404 pages shows URLs that are really 404, there's nothing more to do.