Whenever you don't give us a specific domain to help on, you have to give as much info as possible. On the .com, after you disavowed did you build new authority or just assume the disavow would be enough? (It's not.) On the .com you said you lost traffic January 2013 which is Panda, not Penguin. So you were probably doing a whole lot of link cleanup to solve a problem you can't solve with link cleanup.
Given the other domain isn't ranking either, I'd guess you have some sort of Panda (content) issue. Duplicate content, repetitious & spammy titles, huge keyword stuffed meta keywords tags, thin or non-existent content, etc. Without seeing the site itself it's hard to say but this all reeks of Panda.
As to the questions:
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No, it's not the domain name being similar. Without knowing the domains hard to say about 301.
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Definitely not.