A: Panda is refreshed on a regular basis, if you clean up the areas that need work you will recover.
My Thoughts: Simply creating the same site again with the same content will just be picked up again by Panda. However you could create a new site with new content if you are having trouble finding the issues with your current site, maybe there are more problems than just Panda?
A: YES, John says he RARELY sees any issues and when they do the team will take a look at it and resolve the issues.
My Thoughts: This is a problem because website owners need to be aware of not only links in WMT but also others like Ahrefs and Majestic and keep an eye on them all the time. One of the only ways to help prevent negative SEO is to keep an eye on them all the time.
A: YES, clean up the old link issues with a disavow file or by removing them. If you were ranking well before the penalty and the bad links were the reason then you need to gain new links to replace them or you will remain in a lower postion than before.
My Thoughts: You should make sure that you look at all links not just the ones in WMT otherwise you will get out of the Manual Penalty but still have a Penguin over optimization penalty.
A: YES, however there is more to it. Google needs to have looked at your disavow file and recrawled a large porion of those links so that the index is updated. The penguin refresh or update uses the latest indexed data to calculate how the algorithm will display data.
My Thoughts: This is now much more clear why it is so important to attack your site with a machete as Matt Cutts says
A: No google ignores it completely
My Thoughts: Google may even use this tool to discover what words you are trying to rank for and see if you are doing anything negative to influence it. other searche engines still use this meta tag however.
A: John does not actually answer the question, he tells us that they will not be removed from the index but the links will be marked as nofollow and those links to your site will be dropped.
My Thoughts: We are still unclear if just by those links existance that your site would be worse off than if they were removed.
A: Usually that is not a problem. Anchor text does not automaticlly make a link bad, it depends on many factors such as the site.
My Thoughts: John does not answer the fact that the site could be an exact match domain for keywords, so that could still be a problem.
A: Despite a long conversation about this, John does not answer the question. He gives tips on what to do but does not answer if that thin content would actually hurt rankings.
My Thoughts: I would presume Panda has a problem with that kind of data but John needs to clarify this.
A: John talks about some of the ways the webspam team deals with reconsideration requests.
My Thoughts: If you are heading in the right direction they will release you from the manual penalty.
A: This is not a problem.
My Thoughts: Google has stepped up how they deal with the disavow file and there are lots of checks done to avoid any mistakes you might make.
A: John says definalty NOT, if you provide a good service with different content then you will rank.
My Thoughts: This is a very conflicting message from what various Top Contributors have to says in Google Forums
A: Disavow them as you see them come in, Google is also good at recognising them.
My Thoughts: It is possible that Google only now just found some links that were actually created a long time ago.
A: YES, but it is not gauranteed
My Thoughts: Try using a search engine simulator to see what it finds.