Hello,
Ihave recovered more than 3 websites affected by unnatural link penalty (which is a manual penalty) and used the disavow tool for several clients of mine. Here is what i do recommend for u:
1. Be more determined/accurate with links analysis. You may classify links into 3 groups:
a/definetly spammy: links in footers, sitewides, links from low quality directories, linsk from blog/directory networks, etc...
b/maybe spammy: these are links that appear to be good, but you may have to digg mire to be sure if it's really good (these could be links exhanges, links from websites that have been spotted of seeling links, etc...)
c/good links: this are links using branded anchors, parital matches or low number of exact macth anchors. These links should be placed in relevant websites and high editorial level (not linking to every rubbish oin the web)
About the redirected links, if i were to take this project, i would analyze the redirected links and check if most of them are spammy or have little to no value, i will remove the redirect and take the time and effort to build new links to the .com domain. Creating new links is better than deleting the old ones, here is why:
1. creatinng links is easier and funnier (you feel success when u earn a new good link)
2. it takes less time to see results (disavowing and deleting links may take upt to 3-6 mnths to reflect resullts as google takes time to process these data)
If you have further questions, don't hesitate to get back to me.
Regards
Amine Rihane
SEO Consultant