Had the same issue my own. I actually wrote a couple pieces on that.
After working on hard writing good, shareable content, creating a better user experience, removing those links that might look toxic and then disavowing those that weren't remove, you can go ahead and fill a reconsideration request.
Although those are intended to Websites with a manual action (you received a message in your Webmaster tools), you can still fill that request explaining what happened, what steps you took to solve any possible issue (if any) and ask for some guidance on what is actually going on.
They might not respond, but Google claims ALL requests are read, so if your site has some sort of penalty they will look into it, it could just be a google glitch that they can actually fix.
Take a look at those sites outranking you, are those black hats? if yes, REPORT THEM in that reconsideration request too, or you can use the report feedback form (which is linked to in the same page you post the reconsideration request).
As I said at the beginning, I had the same issue. After fixing everything, sent a reconsideration request pointing all my issues, showing them our efforts, etc, and I don't know if they actually read it, but 2 black hats that were outranking us in page 1, spots #1 and #2 disappeared to page 6 or something like that, so until now (2 days later) it is already paying off!
Hope that helps!