Planet13 - 10:54 pm on Jul 22, 2013 (gmt 0)
I hate to say this but I am a little confused as to all the changes that you have done, and I don't think you have a good idea of the specific links that google finds offensive.
also, even if you do figure out exactly what GOOGLE wants you to do, and you remedy it right anyway, it might take a few more months for you to regain much traffic, and you probably won't get the same level of traffic you had before.
So, just to say what I would do (after researching a LOT about manual penalties and Penguin).
1) Go through all your latest links and disavow any that look even remotely suspiscious - whether they are to your subdomains or main domains or whatever. If in doubt, Disavow them.
2) go through that same disavow file and find whatever pages have ONLY spammy links, then move that page so that page returns a 404 / 410 status.
You probably can't to that with your home page, but there are probably some internal pages (whether on the domain or subdomain) that you can either move to a new subdomain, or a new domain, or just rename the file. Either way, if you think it only has a spammy link, then have it return a 404 / 410.
(And yes, you will be disavowing links to certain pages which you will then move as well so they serve a 404/410 error.)
3) Make another effort to remove bad links pointed at your site by contacting webmasters.
4) Check, double-check, and triple-check that there is no more spam on your sites.
5) After all this, resubmit another reconsideration request.
If you are relying on the disavow tool only, IT COULD TAKE SEVERAL MORE MONTHS before you see any positive results! I read one report and they said it took six months.
The fastest way would be disavow (be sure to use the domain: operator where appropriate), and link removals in conjunction with the reconsideration request.
NOTE: I am not an SEO expert. But I have been studying reports on penalties, Penguins, and disavow files for the last month, so I think I have kind of whittled down the useful info from the b.s. here. Hope this helps.