Planet13 - 4:17 pm on Jul 19, 2013 (gmt 0)
"I was still unable to get out the manual penalty for the main website, probably because the "pharma hack" on my wordpress blogs (on subdomains) is still not completely fixed."
If I understand that there are still hacked pages appearing ON YOUR SITE then you should deal with this first.
" Every 2-3 days GWT shows dozens of 410 errors because new hacked domains are shown and are still linking to those old pages."
Those don't matter. You won't be punished AFAIK for 404 / 410 errors, and if there are a bunch of spammy sites pointing at those 404 pages it SHOULD be ok.
Get your blogs and forum software clean and secure first. You might be able to help speed up by sending a 410 header instead of a 404 header for pages that are gone. Also, you can tell google to remove those pages from the index using GWT (but I don't know how any you can tell them to remove - maybe there is a limit?)
"I didn't document link removal requests because there were about 100 hacked blogs linking to my hacked pages and I'm unable to contact them all. Most of them fixed the hack, some of them didn't."
Did you tell the blog owner that they had been hacked and that they need to update their blog and make it secure? That would be a great way to get those links removed.