Many SEO agencies have strong opinions on reconsideration requests and use of the disavow tool.
So you are in a hole with your organic visitor levels due to previous SEO history. I am uncomfortable with people in SEO pretending that they're whiter than white when really everyone has either experimented or carried out link building that manipulated the SERPs because (a) Google indicated to you to think that everything was down to links and (b) it worked and there was / still is an economy providing loads of cheap links. You've done some link removal work, you've disavowed some links. You've even developed a genuine PR and content marketing plan along with improving on the user experience of your website.
Will submitting a reconsideration request help or work? In the case of the 'unnatural links' message via Google Webmaster Tools, then the answer is yes if you have completely addressed the issue i.e. all of your spammy backlinks have been cleaned up.
So it works...how do you submit your reconsideration request to Google? Sit back and watch Matt Cutts, Head of Web Spam at Google tell you what should be included in a proper reconsideration request:
This Google Webmaster Help video from Cutts can be summarised into 3 main points:
1) You have stopped buying links
2) You have put measures in place to ensure that paid link activity stops (give examples of past 'bad' work and processes that are now in place to prevent spammy SEO from occuring). Use of Google docs (spreadsheets) is recommended for the analysts to view with the knowledge that you are not sending links with malware.
3) Provide a lot of detail of the processes undertaken (the link removal, the disavow and the corrective action moving forward) and convince Google that you are worthy of the penalty being lifted.