tedster - 6:33 pm on Jul 27, 2012 (gmt 0)
If your audience uses Google, and 90+% of mine does...
Then the question becomes, if these URLs are penalized then how much traffic are they still getting? And is the Home Page really relevant for the traffic that comes to an internal page?
Trying to preserve value from URLs that don't get search traffic is what it sounds like to me. It may be that you've thought yourself into a complex knot and there is probably a much simpler solution. Here some more direct approaches.
1. Use the Reconsideration Request to explain the removal requests you made, list which ones were acted on.
2. Just remove those URLs and left the links point to a 404.