aristotle - 9:11 pm on Jul 5, 2012 (gmt 0)
I still don't think Webmaster Tools data is used in the Google algorithm. What if these two websites had never been in Webmaster Tools at all? Would the rankings be different.
By the way, since the old site was doing so well, have you considered deleting the new site, and the re-directs, and reverting back to the old site to see if it would be penalized?