A: John says you need to be creative, and you need content, this question goes on for 15 minutes!
My Thoughts: John really has very little in the way of answers for this topic. This is a problem and Google is unable to deal with it.
A: If it is related then that is OK, do not just use content from other sources.
My Thoughts: I have yet to see this really work, it seems like dropping keywords here and there is the only way unless other SEO factors like the links to your page are strong.
A: Yes use it on both domains to be safe. Submit the same disavow file.
My Thoughts: The disvow tool now alerts you to common mistakes made.
A: In most cases you can do it at the same time.
My Thoughts: it takes time for the Reconsideration Request to be dealt with, so that time is sufficent for the diavow file to be processed. So submit it right away.
A: John Yes you can focus on the links provided in WMT, you 100% definitely do not need third party tools but they can help make it easier.
My Thoughts: The real problem here is that it does not answer the REAL question. What webmasters want to know is if you only fix the issue using link data from WMT will you get out of the link issues you have that will recover your site. The answer to the question is actually NO in many cases as you will have an over optimised link profile and will need to fix that issue. Google only shows you a limited amount of links, for what reason we have no answer just yet. So you may still have problems with penguin and need to clean up all links found in sites like ahrefs and site explorer.
A: YES if there are lots of problems it can add up and cause issues.
My Thoughts: So the answer is to use both WMT and third party tools otehrwise you may just get out of a manual penalty only to be in an over optimized penalty.
A: NO, its just a domain like any other
My Thoughts: Chances are a .com will actually rank better.