1script - 1:54 am on Apr 30, 2013 (gmt 0)
@makin: the message is obviously automated and I do believe the penalty itself, at least since after penguin, is also automatic.
Be careful about admitting to too much sin :) 40% drop these days can come from *anything* - it does not necessarily have to be some Earth shattering black hat technique. Besides, three months between the notice and the drop hint at those two being unrelated. I did have a site receive the "unnatural" notice and not lose any traffic, so chances are your traffic issue may not even be related to the notice.
560 domains pointing to one is something I never heard of and have no experience in dealing with. If you said 3, I would say, have them all authenticated with WMT (using DNS TXT record) and move them to the destination domain properly i.e. via WMT-> Configurarion -> Change of Address
But I would have no idea how to scale that to 560 - sorry.
As far as the number of links (domains?) in the disavow file - there are rumors that noone actually looks at those at the present. They kinda sorta just gather information at this point. So, I would assume it does not matter much how long is your list, they just want to see as many of those bad links ACTUALLY removed. Not disavowed but really removed. I was only successful when I was able to actually remove large proportion of bad links. Well, in my case many bad links were transient and the sites expired, so the links were gone.