MLM,
1. Per Google, just disavowing links isn't enough to make your reconsideration request successful, G also wants to see a good faith effort to get your toxic links removed whenever possible.
2. If a site no longer exists and the pages that contain links to your site not longer exist, it may take some time for them to disappear from the crawl indexes but you won't have to do anything about them--the links are non-existent.
3.For purposes of your reinclusion request, you should make note of the fact that the sites were marked as malicious and include those links in your disavow link file.
4. If you have reason to believe that the links on those foreign sites are inorganic you can still attempt to contact the webmaster with your removal request, and if no response, add them to your disavow link file.
5. Its my conjecture that effective negative SEO is likely to be as expensive as link building for your own site, which means that someone going out and buying a bunch of low quality links and pointing them at your site is not going to do anything. It's the links that cross a certain threshold of strength AND fit the mold of inorganic that trip the filter. Once tripped, however, the owner is stuck with cleaning up the whole mess.
6. Don't worry about anchor text within your own site, as long as it's not crazy ridiculous.
If it was my site, I'd be focusing on whether it was panda or not. A site with a penquin penalty may be salvageable but one with a panda penalty may not be. As far as your toxic links, don't forget you can move your linked-to content to new URLs and leave the old ones to 404--it's an option if you don't have bad ones pointing to your home page. 301ing to a new domain is generally considered to eventually redirect your penalty to the new domain as well, so I wouldn't go that route.