Disavow- What Happens and What Should I Do?

[Fuel]

We have a site that got hit by a non-manual penalty in July really hard. I submitted a disavow file for the site placeyourlinks.com which had a bunch of clearly spammy links to the site listed in Webmaster tools. But the site itself was down for a long time so I couldn't see where the links even were. Then those links disappeared from the links file. I thought the urls were removed or the site was seen as being blank. But now they're back...and the site itself is shown as just being a blank page. I don't know what to do since I don't want to disavow those links again if it wasn't even addressed the first time and there is obviously no way to contact the site. Help!

Also, I've done a bunch of work on the site to increase the amount of content while I was waiting to see what happened with the link disavow. But now all that is done and our rankings are still waaaay down. I'm considering getting really, really aggressive with link removal and disavowing if needed but I'm not sure what I should focus on removing/disavowing. Really bad sites with only one or two links? Sites that have a lot of links to the site? Sites with keyword stuffy anchor text? Any help on this would be much appreciated.

[MikeRoberts]

Had you received an unnatural links warning at all? Usually people suggest not using the Disavow Tool unless you've received that warning. What does your link profile look like? And have you worked on gaining more relevant links and social signals in the time being? If it was an algorithmic penalty in July then it was possibly Panda related but, as I don't have any more information to go on, that's just speculation. Assuming it was Panda then your main issue was likely thin content not links. How does your site look concerning duplicate content, spammy content, and thin pages?