Recovery from Link Penalty (manual or algorithm) procedure:
1. Collect inboud links from Google Webmaster Tools + Moz link explorer + Link Majestic.
2. Include all domains in a Excel worksheet.
3. Contact site owners asking for link removal (usually 5% of sucess, but the effort counts for Google).
4. Wait several weeks for the removal of the links.
5. Fill a disavow file and upload it to Google https://www.google.com/webmasters/tools/disavow-links-main?pli=1
6. Wait for 3 or 6 weeks and start a link building campain starting with a few links per week and increase it if you can (only natural links comming from authority sites related to your niche).
Recovers from Content problems.
1. Look for repetitive title and descriptions, use Google Webmaster Tools and Moz.
2. Look for pages with similar or identical content and fix it.
3. Look for pages with less than 200 words of convent and add content or simply remove them (404).
4. Add new fresh and original content.
Google will consider your effort and it will be increasing your rank step by step.
I hope it helps
Claudio