Our site was handed a manual penalty in November 2013 where exact match anchor text and low quality directory submissions seemed to be the problem. We began the process of link removal, reconfiguration and disavowing.
We had already planned to change our domain in early 2014 to coincide with our SSL certificate renewal and although we were hesitant to do this with the manual penalty still there we proceeded and 301'd most of the site but left the pages that were the landing page for most of the exact match links as 302 to the new domain.
We continued to work on removing the manual penalty for the old domain as we didn't want it to pass over to the new one and eventually this was removed n March 2014
Now the penalty is gone are we safe to change those 302 redirects to 301 so everything redirects. The problem we have is that six months on, a lot of the pages for the old domain are still indexed and even though we are indexed for the new domains are rankings haven't recovered.
Is it just a case of needing to build up a new quality link profile to replace the links that were disregarded or removed when recovering from the penalty or we missing something else