I haven't been given any manual penalty from Google (well, not that I am aware of anyway). However, we have lots of poor quality sites and directories linking to us (we've been running since 2001).
Following poor performance in the SERPs over the past year or so, we decided to go through each and every link and disavow anything that looked spammy or low quality or was a directory site.
This took us hours.
We submitted it to Google back in August 2013, but since then, NOTHING! The links we've disavowed are still showing in webmaster tools and rankings continue to fall.
Is there anything else we can do - why would the file be ignored?