I know this is an old post - but I am one of those who received the notice, and then engaged GOOGLE as I tried to ascertain what was going on, and what links they were referring to. The links were part of a link network that I had experimented with - I set it and forgot all about it - till the notification. The links were REALLY bad, I would never even have tested it had I known how bad they were going to be (like content that was totally irrelevant to my content!) so GOOGLE did me a favor, but it was sort of like taking your medicine - it hurt going down let me tell you.
It took me 4-6 weeks to find and get the sites that were bad removed. They were removed. My rankings for the specific terms that were used in those links are still hosed. Overall, my site took a hit, and some of my work I hope has resulted in some recovery - but it's very hard to tell.
I do think that removing all the bad links did hurt my site as badly as the google manual action.
To answer the questions - yes, the google team worked with me, yes, they answered my questions and emails and yes, the acknowledged that the manual action was removed.
It's been bad for me, this panda thing, and I've had to really work at other stuff to keep my revenue stream up - I'm down about 20% but it's also hard to tell because we are sort of seasonal as well and this is our slow period. But I'm pretty sure our fuzzy butts were kicked by panda/penquin, whatever.