1/ Unnatural inbound links message does not lead necessarily to a loss of rank and a loss of traffic. Even SEOmoz.org got the same message and lost nothing (http://www.seomoz.org/blog/googles-unnatural-links-warnings). I had the same experience for a flash game website.
2/ If you actually lost ranks/traffic, you have to show your good will and give something to Google. I suggest you to use Open Site Explorer and to look for low authority linking domains.
Example : last URL = www.cheapautoexpo.com/tag/coupons/
You have 4 links on the same page - deals365.us did the same. A click = a pop-up. This looks like a bad neighbourhood.
You won't lose much by removing this kind of links. Keep a track of all the links you removed. In this case :
http://www.cheapautoexpo.com/Lifestyle/verified-online-promo-codes-for-discounts-on-apparels-shopping/
http://www.cheapautoexpo.com/News/get-discounts-on-concert-tickets-through-with-ticket-spot-coupon-codes/
http://www.cheapautoexpo.com/Education/revolution-prep-promo-codes-coupons-to-learn-sat-act-at-affordable-price-online-/
http://www.cheapautoexpo.com/Lifestyle/get-expedia-promo-codes-coupons-to-have-cheap-tickets-for-travel-and-hotels-/
It will show Google you did a serious work.
3/ If you can't remove the links manually, ask the webmaster to do it. In most cases he won't answer if this is a spammy website.
Then consider using the disallow tool : https://www.google.com/webmasters/tools/disavow-links-main?pli=1
4/ I would recommend you to do the same for all the low directories... and the link suggested by Google : http://www.allworldlinks.com/k/317277/online-free-coupons.html
5/ Pinpoint Designs had the same issue and wrote and article about : http://www.seomoz.org/blog/lifting-a-manual-penalty-given-by-google-personal-experience
In the reconsideration request, they mentionned :
- Who we were and what we do
- Why we believed we had been hit
- What we had done to rectify the issue (a link to the Google Docs file was attached)
- How we knew it wouldn't happen again
- An apology
- My name / contact details
They also tried to improve the quality of their website (do you have good content on your website or just coupons ?) and to get better links; they started a blog and wrote guest articles.
6/ To get better links, I suggest you to use open site explorer on competitors to see their most authoritative links. Most of time, you can also get the same link if this is a directory or a blog taking guest posts.
7/ Last but not least, Google spam team is human. Your reconsideration request depends of the employee who will deal with it... You can never be sure of the result.
Good luck ~~.